run_metadata
245 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Endocrine System"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 33294 | 33294 | SRR29920543 | SRX25414719 | SRS22075127 | SRP521426 | PRJNA1138768 | Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics | GSE272806 | Transcriptome Analysis | Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish however is an exception as gnrh3–/– fish which lack the hypophysiotropic GnRH3 are fertile suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2 thyroid hormone estrogen dopamine and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes instead the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2 but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression probably via a non Gnrh receptor route. Altogether while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing | pubmed:39499852 | gnrh3 knockout scRNAseq | GSM8412848 | source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female|geo loc name:missing|collection date:missing | gnrh3 knockout scRNAseq | Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control normalization data integration and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files matrix file and comma separated values file | Pituitary | Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample. | tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female | GSM8412848 | GSM8412848: gnrh3 knockout scRNAseq; Danio rerio; RNA Seq | GSM8412848 r1 | GSM8412848 | 1 | Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP521426 | loader:fastq load.py | KO_20210616_A00904_IL100185604_S1_L001_I1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_I2_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R2_001.fastq.gz | fastq fastq fastq fastq | 27063230346.0 | 121906443.0 | GSM8412848 r1 | 0:10 1:10 2:101 3:101 | A:6434793761;C:4051189285;G:4401327014;T:9737249538;N:541888 | 10 | 10 | 101 | 101 | 6434793761 | 4051189285 | 4401327014 | 9737249538 | 541888 | SRX25414719 | SRS22075127 | SRA1930291 | Stanford University | Stanford University | 2 | 0.10559 | 0.92046 | 0.02334 | 0.15386 | 0.97879 | 0.81732 | 0.68611 | 0.62975 | 101 | 101 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-07-22 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||
| 33295 | 33295 | SRR29920544 | SRX25414718 | SRS22075126 | SRP521426 | PRJNA1138768 | Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics | GSE272806 | Transcriptome Analysis | Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish however is an exception as gnrh3–/– fish which lack the hypophysiotropic GnRH3 are fertile suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2 thyroid hormone estrogen dopamine and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes instead the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2 but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression probably via a non Gnrh receptor route. Altogether while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing | pubmed:39499852 | WT scRNAseq | GSM8412847 | source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:wild type|Sex:female|geo loc name:missing|collection date:missing | WT scRNAseq | Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control normalization data integration and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files matrix file and comma separated values file | Pituitary | Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample. | tissue:Pituitary|age:Adult 3 mpf|genotype:wild type|Sex:female | GSM8412847 | GSM8412847: WT scRNAseq; Danio rerio; RNA Seq | GSM8412847 r1 | GSM8412847 | 1 | Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP521426 | loader:fastq load.py | WT_20210616_A00904_IL100185603_S1_L001_I1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_I2_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R2_001.fastq.gz | fastq fastq fastq fastq | 26784946020.0 | 120652910.0 | GSM8412847 r1 | 0:10 1:10 2:101 3:101 | A:6396247260;C:3989076165;G:4295547390;T:9690479627;N:537378 | 10 | 10 | 101 | 101 | 6396247260 | 3989076165 | 4295547390 | 9690479627 | 537378 | SRX25414718 | SRS22075126 | SRA1930291 | Stanford University | Stanford University | 2 | 0.10896 | 0.92399 | 0.02311 | 0.16455 | 0.97652 | 0.80377 | 0.67721 | 0.64804 | 101 | 101 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-07-22 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||
| 34324 | 34324 | SRR31647630 | SRX27010714 | SRS23475005 | SRP550229 | PRJNA1195876 | Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq] | GSE283840 | Transcriptome Analysis | Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically Amh binds to its receptors Bmpr2a/Bmpr1bb which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis. | pubmed:40348785 | pituitary gland Amh KO | GSM8672964 | source name:pituitary gland|tissue:pituitary gland|genotype:knockout Amh|geo loc name:missing|collection date:missing | pituitary gland Amh KO | Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files | pituitary gland | post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer’s solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions. | tissue:pituitary gland|genotype:knockout Amh | GSM8672964 | GSM8672964: pituitary gland Amh KO; Danio rerio; RNA Seq | GSM8672964 r1 | GSM8672964 | 1 | post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer's solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP550229 | Amh_KO_R1.fq.gz Amh_KO_R2.fq.gz | fastq fastq | 154810080300.0 | 516033601.0 | GSM8672964 r1 | 0:150 1:150 | A:51891488591;C:26616629262;G:25307529846;T:50992970078;N:1462523 | 150 | 150 | 51891488591 | 26616629262 | 25307529846 | 50992970078 | 1462523 | SRX27010714 | SRS23475005 | SRA2029986 | Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences | Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2024-12-09 | Undetermined | Undetermined | Pituitary Gland | Endocrine System | |||||||||||||||||||||||
| 34325 | 34325 | SRR31647631 | SRX27010713 | SRS23475006 | SRP550229 | PRJNA1195876 | Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq] | GSE283840 | Transcriptome Analysis | Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically Amh binds to its receptors Bmpr2a/Bmpr1bb which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis. | pubmed:40348785 | pituitary gland WT | GSM8672963 | source name:pituitary gland|tissue:pituitary gland|genotype:WT|geo loc name:missing|collection date:missing | pituitary gland WT | Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files | pituitary gland | post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer’s solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions. | tissue:pituitary gland|genotype:WT | GSM8672963 | GSM8672963: pituitary gland WT; Danio rerio; RNA Seq | GSM8672963 r1 | GSM8672963 | 1 | post dissection zebrafish pituitaries from WT or amh / females were washed with cold PBS or fresh Ringer's solution for 5 10 min followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies 400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer centrifuged 2000 rpm 5 min 4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP550229 | WT_R1.fq.gz WT_R2.fq.gz | fastq fastq | 149500940700.0 | 498336469.0 | GSM8672963 r1 | 0:150 1:150 | A:49714239420;C:27445649314;G:26079818385;T:46259970208;N:1263373 | 150 | 150 | 49714239420 | 27445649314 | 26079818385 | 46259970208 | 1263373 | SRX27010713 | SRS23475006 | SRA2029986 | Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences | Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2024-12-09 | Undetermined | Undetermined | Pituitary Gland | Endocrine System | |||||||||||||||||||||||
| 69988 | 69988 | SRR19217299 | SRX15281308 | SRS13012753 | SRP375342 | PRJNA838481 | Neural plate progenitors give rise to both anterior and posterior pituitary cells | GSE203075 | Transcriptome Analysis | The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group. | pubmed:37683631 | AB9278 | GSM6153483 | source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing | AB9278 | bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster | Neurohypophysis enriched cells | 5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below. | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | 37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility. | strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month | GSM6153483 | GSM6153483: AB9278; Danio rerio; RNA Seq | GSM6153483 r1 | GSM6153483 | 1 | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP375342 | loader:fastq load.py | AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz | fastq fastq | 1259447780.0 | 11770540.0 | GSM6153483 r1 | 0:92 1:15 | A:305608913;C:313550706;G:363197186;T:277079546;N:11429 | 92 | 15 | 305608913 | 313550706 | 363197186 | 277079546 | 11429 | SRX15281308 | SRS13012753 | SRA1420605 | Molecular Cell Biology, Weizmann Institute of Science | Molecular Cell Biology, Weizmann Institute of Science | 2 | 0.94767 | 0.0 | 0.32091 | 0.0 | 0.89796 | 1.0 | 0.7545 | 92 | 15 | B | T | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | marsseq | Israel | 2022-05-16 | Adult | Adult | Pituitary Gland | Endocrine System | ||||||||||
| 69989 | 69989 | SRR19217300 | SRX15281307 | SRS13012752 | SRP375342 | PRJNA838481 | Neural plate progenitors give rise to both anterior and posterior pituitary cells | GSE203075 | Transcriptome Analysis | The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group. | pubmed:37683631 | AB9277 | GSM6153482 | source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing | AB9277 | bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster | Neurohypophysis enriched cells | 5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below. | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | 37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility. | strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month | GSM6153482 | GSM6153482: AB9277; Danio rerio; RNA Seq | GSM6153482 r1 | GSM6153482 | 1 | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP375342 | loader:fastq load.py | AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz | fastq fastq | 1130776107.0 | 10568001.0 | GSM6153482 r1 | 0:92 1:15 | A:288600700;C:269726443;G:310844405;T:261594352;N:10207 | 92 | 15 | 288600700 | 269726443 | 310844405 | 261594352 | 10207 | SRX15281307 | SRS13012752 | SRA1420605 | Molecular Cell Biology, Weizmann Institute of Science | Molecular Cell Biology, Weizmann Institute of Science | 2 | 0.94379 | 0.0 | 0.28638 | 0.0 | 0.86415 | 1.0 | 0.63321 | 92 | 15 | B | T | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | marsseq | Israel | 2022-05-16 | Adult | Adult | Pituitary Gland | Endocrine System | ||||||||||
| 69990 | 69990 | SRR19217301 | SRX15281306 | SRS13012751 | SRP375342 | PRJNA838481 | Neural plate progenitors give rise to both anterior and posterior pituitary cells | GSE203075 | Transcriptome Analysis | The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group. | pubmed:37683631 | AB9280 | GSM6153481 | source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing | AB9280 | bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster | Neurohypophysis enriched cells | 5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below. | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | 37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility. | strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month | GSM6153481 | GSM6153481: AB9280; Danio rerio; RNA Seq | GSM6153481 r1 | GSM6153481 | 1 | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP375342 | loader:fastq load.py | AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz | fastq fastq | 1172966528.0 | 10962304.0 | GSM6153481 r1 | 0:92 1:15 | A:311089180;C:274626206;G:310304031;T:276936052;N:11059 | 92 | 15 | 311089180 | 274626206 | 310304031 | 276936052 | 11059 | SRX15281306 | SRS13012751 | SRA1420605 | Molecular Cell Biology, Weizmann Institute of Science | Molecular Cell Biology, Weizmann Institute of Science | 2 | 0.92936 | 0.0 | 0.23628 | 0.0 | 0.86147 | 1.0 | 0.74656 | 92 | 15 | B | T | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | marsseq | Israel | 2022-05-16 | Adult | Adult | Pituitary Gland | Endocrine System | ||||||||||
| 69991 | 69991 | SRR19217302 | SRX15281305 | SRS13012750 | SRP375342 | PRJNA838481 | Neural plate progenitors give rise to both anterior and posterior pituitary cells | GSE203075 | Transcriptome Analysis | The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group. | pubmed:37683631 | AB9279 | GSM6153480 | source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing | AB9279 | bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster | Neurohypophysis enriched cells | 5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below. | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | 37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility. | strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month | GSM6153480 | GSM6153480: AB9279; Danio rerio; RNA Seq | GSM6153480 r1 | GSM6153480 | 1 | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP375342 | loader:fastq load.py | AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz | fastq fastq | 1383147163.0 | 12926609.0 | GSM6153480 r1 | 0:92 1:15 | A:364575971;C:320901229;G:367626618;T:330030659;N:12686 | 92 | 15 | 364575971 | 320901229 | 367626618 | 330030659 | 12686 | SRX15281305 | SRS13012750 | SRA1420605 | Molecular Cell Biology, Weizmann Institute of Science | Molecular Cell Biology, Weizmann Institute of Science | 2 | 0.92462 | 0.0 | 0.26743 | 0.0 | 0.8493 | 1.0 | 0.74133 | 92 | 15 | B | T | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | marsseq | Israel | 2022-05-16 | Adult | Adult | Pituitary Gland | Endocrine System | ||||||||||
| 69992 | 69992 | SRR19217303 | SRX15281304 | SRS13012749 | SRP375342 | PRJNA838481 | Neural plate progenitors give rise to both anterior and posterior pituitary cells | GSE203075 | Transcriptome Analysis | The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group. | pubmed:37683631 | AB7418 | GSM6153479 | source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing | AB7418 | bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster | Neurohypophysis enriched cells | 5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below. | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | 37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility. | strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf | GSM6153479 | GSM6153479: AB7418; Danio rerio; RNA Seq | GSM6153479 r1 | GSM6153479 | 1 | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP375342 | AB7418_SB350_S35_R1_001.fastq.gz AB7418_SB350_S35_R2_001.fastq.gz | fastq fastq | 2468773944.0 | 29390166.0 | GSM6153479 r1 | 0:69 1:15 | A:764359919;C:520031317;G:592699381;T:591594655;N:88672 | 69 | 15 | 764359919 | 520031317 | 592699381 | 591594655 | 88672 | SRX15281304 | SRS13012749 | SRA1420605 | Molecular Cell Biology, Weizmann Institute of Science | Molecular Cell Biology, Weizmann Institute of Science | 2 | 0.85786 | 0.0 | 0.15143 | 0.0 | 0.84885 | 1.0 | 0.67021 | 69 | 15 | B | T | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | marsseq | Israel | 2022-05-16 | Juvenile | Juvenile | Pituitary Gland | Endocrine System | |||||||||||
| 69993 | 69993 | SRR19217304 | SRX15281303 | SRS13012748 | SRP375342 | PRJNA838481 | Neural plate progenitors give rise to both anterior and posterior pituitary cells | GSE203075 | Transcriptome Analysis | The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group. | pubmed:37683631 | AB7417 | GSM6153478 | source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing | AB7417 | bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method="LogNormalize" scale.factor= 10000 and ScaleData vars.to.regress = c"nCount RNA" "percent.mito". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = "pca" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster | Neurohypophysis enriched cells | 5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below. | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | 37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility. | strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf | GSM6153478 | GSM6153478: AB7417; Danio rerio; RNA Seq | GSM6153478 r1 | GSM6153478 | 1 | 5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP375342 | AB7417_SB350_S24_R1_001.fastq.gz AB7417_SB350_S24_R2_001.fastq.gz | fastq fastq | 2586526488.0 | 30791982.0 | GSM6153478 r1 | 0:69 1:15 | A:833353097;C:525447349;G:601496569;T:626135990;N:93483 | 69 | 15 | 833353097 | 525447349 | 601496569 | 626135990 | 93483 | SRX15281303 | SRS13012748 | SRA1420605 | Molecular Cell Biology, Weizmann Institute of Science | Molecular Cell Biology, Weizmann Institute of Science | 2 | 0.84125 | 0.0 | 0.10717 | 0.0 | 0.84768 | 1.0 | 0.63154 | 69 | 15 | B | T | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | marsseq | Israel | 2022-05-16 | Juvenile | Juvenile | Pituitary Gland | Endocrine System | |||||||||||
| 74411 | 74411 | SRR23929935 | SRX19740082 | SRS17106156 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 029 10 dy post single ablation | GSM7085299 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | 10X 22 029 10 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | GSM7085299 | GSM7085299: 10X 22 029 10 dy post single ablation; Danio rerio; RNA Seq | GSM7085299 r1 | GSM7085299 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5005_S5_L002_R1_001.fastq.gz P25452_5005_S5_L002_R2_001.fastq.gz | fastq fastq | 15981848610.0 | 135439395.0 | GSM7085299 r1 | 0:28 1:90 | A:4477963598;C:3506223270;G:3720138896;T:4272649273;N:4873573 | 28 | 90 | 4477963598 | 3506223270 | 3720138896 | 4272649273 | 4873573 | SRX19740082 | SRS17106156 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.04362 | 0.92756 | 0.00827 | 0.05019 | 0.96735 | 0.82235 | 0.52602 | 0.51548 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74412 | 74412 | SRR23929936 | SRX19740082 | SRS17106156 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 029 10 dy post single ablation | GSM7085299 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | 10X 22 029 10 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | GSM7085299 | GSM7085299: 10X 22 029 10 dy post single ablation; Danio rerio; RNA Seq | GSM7085299 r1 | GSM7085299 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5005_S5_L001_R1_001.fastq.gz P25452_5005_S5_L001_R2_001.fastq.gz | fastq fastq | 15668510938.0 | 132783991.0 | GSM7085299 r2 | 0:28 1:90 | A:4395565570;C:3432293178;G:3641398206;T:4194659976;N:4594008 | 28 | 90 | 4395565570 | 3432293178 | 3641398206 | 4194659976 | 4594008 | SRX19740082 | SRS17106156 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.04195 | 0.92568 | 0.00791 | 0.05081 | 0.96907 | 0.82457 | 0.52113 | 0.50458 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74413 | 74413 | SRR23929937 | SRX19740081 | SRS17106155 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 028 10 dy post single ablation | GSM7085298 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | 10X 22 028 10 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | GSM7085298 | GSM7085298: 10X 22 028 10 dy post single ablation; Danio rerio; RNA Seq | GSM7085298 r1 | GSM7085298 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5004_S4_L002_R1_001.fastq.gz P25452_5004_S4_L002_R2_001.fastq.gz | fastq fastq | 19699197418.0 | 166942351.0 | GSM7085298 r1 | 0:28 1:90 | A:5698419662;C:4261860362;G:4502693367;T:5230229242;N:5994785 | 28 | 90 | 5698419662 | 4261860362 | 4502693367 | 5230229242 | 5994785 | SRX19740081 | SRS17106155 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.01071 | 0.90569 | 0.00273 | 0.11561 | 0.98654 | 0.78792 | 0.40331 | 0.53787 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74414 | 74414 | SRR23929938 | SRX19740081 | SRS17106155 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 028 10 dy post single ablation | GSM7085298 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | 10X 22 028 10 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation | GSM7085298 | GSM7085298: 10X 22 028 10 dy post single ablation; Danio rerio; RNA Seq | GSM7085298 r1 | GSM7085298 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5004_S4_L001_R1_001.fastq.gz P25452_5004_S4_L001_R2_001.fastq.gz | fastq fastq | 19264495566.0 | 163258437.0 | GSM7085298 r2 | 0:28 1:90 | A:5579106248;C:4162230591;G:4396617008;T:5120939377;N:5602342 | 28 | 90 | 5579106248 | 4162230591 | 4396617008 | 5120939377 | 5602342 | SRX19740081 | SRS17106155 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.01049 | 0.9064 | 0.00254 | 0.11668 | 0.98802 | 0.78819 | 0.38795 | 0.5416 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74415 | 74415 | SRR23929939 | SRX19740080 | SRS17106154 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 023 2 dy post double ablation | GSM7085297 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | 10X 22 023 2 dy post double ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | GSM7085297 | GSM7085297: 10X 22 023 2 dy post double ablation; Danio rerio; RNA Seq | GSM7085297 r1 | GSM7085297 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5002_S2_L002_R1_001.fastq.gz P25452_5002_S2_L002_R2_001.fastq.gz | fastq fastq | 21576552402.0 | 182852139.0 | GSM7085297 r1 | 0:28 1:90 | A:6042712664;C:4829068008;G:5090500060;T:5607976659;N:6295011 | 28 | 90 | 6042712664 | 4829068008 | 5090500060 | 5607976659 | 6295011 | SRX19740080 | SRS17106154 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00738 | 0.92586 | 0.00228 | 0.09935 | 0.99121 | 0.79484 | 0.3212 | 0.51367 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74416 | 74416 | SRR23929940 | SRX19740080 | SRS17106154 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 023 2 dy post double ablation | GSM7085297 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | 10X 22 023 2 dy post double ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | GSM7085297 | GSM7085297: 10X 22 023 2 dy post double ablation; Danio rerio; RNA Seq | GSM7085297 r1 | GSM7085297 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5002_S2_L001_R1_001.fastq.gz P25452_5002_S2_L001_R2_001.fastq.gz | fastq fastq | 21225949858.0 | 179880931.0 | GSM7085297 r2 | 0:28 1:90 | A:5950173859;C:4745833170;G:5001820306;T:5522228778;N:5893745 | 28 | 90 | 5950173859 | 4745833170 | 5001820306 | 5522228778 | 5893745 | SRX19740080 | SRS17106154 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00726 | 0.92674 | 0.00215 | 0.10093 | 0.99176 | 0.79527 | 0.29771 | 0.53423 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74417 | 74417 | SRR23929941 | SRX19740079 | SRS17106153 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 022 2 dy post double ablation | GSM7085296 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | 10X 22 022 2 dy post double ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | GSM7085296 | GSM7085296: 10X 22 022 2 dy post double ablation; Danio rerio; RNA Seq | GSM7085296 r1 | GSM7085296 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5001_S1_L002_R1_001.fastq.gz P25452_5001_S1_L002_R2_001.fastq.gz | fastq fastq | 44183541338.0 | 374436791.0 | GSM7085296 r1 | 0:28 1:90 | A:12516849477;C:9732461815;G:10343631784;T:11577097367;N:13500895 | 28 | 90 | 12516849477 | 9732461815 | 10343631784 | 11577097367 | 13500895 | SRX19740079 | SRS17106153 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00804 | 0.91216 | 0.00229 | 0.10832 | 0.9906 | 0.79539 | 0.33148 | 0.51054 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74418 | 74418 | SRR23929942 | SRX19740079 | SRS17106153 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 022 2 dy post double ablation | GSM7085296 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | 10X 22 022 2 dy post double ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation | GSM7085296 | GSM7085296: 10X 22 022 2 dy post double ablation; Danio rerio; RNA Seq | GSM7085296 r1 | GSM7085296 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_5001_S1_L001_R1_001.fastq.gz P25452_5001_S1_L001_R2_001.fastq.gz | fastq fastq | 43501281740.0 | 368654930.0 | GSM7085296 r2 | 0:28 1:90 | A:12337254735;C:9571145572;G:10170136596;T:11410054623;N:12690214 | 28 | 90 | 12337254735 | 9571145572 | 10170136596 | 11410054623 | 12690214 | SRX19740079 | SRS17106153 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00811 | 0.91214 | 0.00243 | 0.10798 | 0.99042 | 0.79299 | 0.27117 | 0.51073 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74419 | 74419 | SRR23929943 | SRX19740078 | SRS17106152 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 021 2 dy post single ablation | GSM7085295 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | 10X 22 021 2 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | GSM7085295 | GSM7085295: 10X 22 021 2 dy post single ablation; Danio rerio; RNA Seq | GSM7085295 r1 | GSM7085295 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2008_S8_L001_R1_001.fastq.gz P25452_2008_S8_L001_R2_001.fastq.gz | fastq fastq | 10399611282.0 | 88132299.0 | GSM7085295 r1 | 0:28 1:90 | A:2977005008;C:2261455885;G:2402621333;T:2758168947;N:360109 | 28 | 90 | 2977005008 | 2261455885 | 2402621333 | 2758168947 | 360109 | SRX19740078 | SRS17106152 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00664 | 0.91101 | 0.00219 | 0.14269 | 0.9903 | 0.71492 | 0.31124 | 0.52378 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74420 | 74420 | SRR23929944 | SRX19740078 | SRS17106152 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 021 2 dy post single ablation | GSM7085295 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | 10X 22 021 2 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | GSM7085295 | GSM7085295: 10X 22 021 2 dy post single ablation; Danio rerio; RNA Seq | GSM7085295 r1 | GSM7085295 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2008_S8_L002_R1_001.fastq.gz P25452_2008_S8_L002_R2_001.fastq.gz | fastq fastq | 10469509172.0 | 88724654.0 | GSM7085295 r2 | 0:28 1:90 | A:2996060103;C:2277562123;G:2419801341;T:2775787165;N:298440 | 28 | 90 | 2996060103 | 2277562123 | 2419801341 | 2775787165 | 298440 | SRX19740078 | SRS17106152 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00668 | 0.91267 | 0.00218 | 0.14377 | 0.98942 | 0.71571 | 0.30058 | 0.51379 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74421 | 74421 | SRR23929945 | SRX19740077 | SRS17106151 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 020 2 dy post single ablation | GSM7085294 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | 10X 22 020 2 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | GSM7085294 | GSM7085294: 10X 22 020 2 dy post single ablation; Danio rerio; RNA Seq | GSM7085294 r1 | GSM7085294 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2007_S7_L002_R1_001.fastq.gz P25452_2007_S7_L002_R2_001.fastq.gz | fastq fastq | 12171375736.0 | 103147252.0 | GSM7085294 r1 | 0:28 1:90 | A:3516523748;C:2630891316;G:2846235380;T:3177374207;N:351085 | 28 | 90 | 3516523748 | 2630891316 | 2846235380 | 3177374207 | 351085 | SRX19740077 | SRS17106151 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00723 | 0.88579 | 0.00253 | 0.14244 | 0.98955 | 0.73241 | 0.30415 | 0.52544 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74422 | 74422 | SRR23929946 | SRX19740077 | SRS17106151 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 020 2 dy post single ablation | GSM7085294 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | 10X 22 020 2 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation | GSM7085294 | GSM7085294: 10X 22 020 2 dy post single ablation; Danio rerio; RNA Seq | GSM7085294 r1 | GSM7085294 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2007_S7_L001_R1_001.fastq.gz P25452_2007_S7_L001_R2_001.fastq.gz | fastq fastq | 12113839290.0 | 102659655.0 | GSM7085294 r2 | 0:28 1:90 | A:3500990622;C:2617308142;G:2831547053;T:3163575276;N:418197 | 28 | 90 | 3500990622 | 2617308142 | 2831547053 | 3163575276 | 418197 | SRX19740077 | SRS17106151 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00769 | 0.88714 | 0.00281 | 0.14223 | 0.98904 | 0.73127 | 0.27861 | 0.53047 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74423 | 74423 | SRR23929947 | SRX19740076 | SRS17106150 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 019 no ablation | GSM7085293 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | 10X 22 019 no ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | GSM7085293 | GSM7085293: 10X 22 019 no ablation; Danio rerio; RNA Seq | GSM7085293 r1 | GSM7085293 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2006_S6_L002_R1_001.fastq.gz P25452_2006_S6_L002_R2_001.fastq.gz | fastq fastq | 26823163746.0 | 227314947.0 | GSM7085293 r1 | 0:28 1:90 | A:7462514069;C:6054472155;G:6429173301;T:6876229429;N:774792 | 28 | 90 | 7462514069 | 6054472155 | 6429173301 | 6876229429 | 774792 | SRX19740076 | SRS17106150 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00659 | 0.91951 | 0.0022 | 0.12919 | 0.99222 | 0.78677 | 0.35595 | 0.57041 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74424 | 74424 | SRR23929948 | SRX19740076 | SRS17106150 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 019 no ablation | GSM7085293 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | 10X 22 019 no ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | GSM7085293 | GSM7085293: 10X 22 019 no ablation; Danio rerio; RNA Seq | GSM7085293 r1 | GSM7085293 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2006_S6_L001_R1_001.fastq.gz P25452_2006_S6_L001_R2_001.fastq.gz | fastq fastq | 26613584654.0 | 225538853.0 | GSM7085293 r2 | 0:28 1:90 | A:7408899229;C:6002907526;G:6374299140;T:6826557518;N:921241 | 28 | 90 | 7408899229 | 6002907526 | 6374299140 | 6826557518 | 921241 | SRX19740076 | SRS17106150 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00675 | 0.91914 | 0.00208 | 0.12941 | 0.99172 | 0.78711 | 0.31131 | 0.54926 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74425 | 74425 | SRR23929949 | SRX19740075 | SRS17106149 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 018 no ablation | GSM7085292 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | 10X 22 018 no ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | GSM7085292 | GSM7085292: 10X 22 018 no ablation; Danio rerio; RNA Seq | GSM7085292 r1 | GSM7085292 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2005_S5_L001_R1_001.fastq.gz P25452_2005_S5_L001_R2_001.fastq.gz | fastq fastq | 28788320170.0 | 243968815.0 | GSM7085292 r1 | 0:28 1:90 | A:8028169272;C:6492038211;G:6870412969;T:7396707337;N:992381 | 28 | 90 | 8028169272 | 6492038211 | 6870412969 | 7396707337 | 992381 | SRX19740075 | SRS17106149 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00685 | 0.91809 | 0.00218 | 0.13019 | 0.99186 | 0.78374 | 0.33856 | 0.54827 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74426 | 74426 | SRR23929950 | SRX19740075 | SRS17106149 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 018 no ablation | GSM7085292 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | 10X 22 018 no ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation | GSM7085292 | GSM7085292: 10X 22 018 no ablation; Danio rerio; RNA Seq | GSM7085292 r1 | GSM7085292 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2005_S5_L002_R1_001.fastq.gz P25452_2005_S5_L002_R2_001.fastq.gz | fastq fastq | 29018537226.0 | 245919807.0 | GSM7085292 r2 | 0:28 1:90 | A:8087164697;C:6548645987;G:6930820281;T:7451072090;N:834171 | 28 | 90 | 8087164697 | 6548645987 | 6930820281 | 7451072090 | 834171 | SRX19740075 | SRS17106149 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00688 | 0.91748 | 0.00228 | 0.13154 | 0.99184 | 0.78344 | 0.35287 | 0.56374 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74427 | 74427 | SRR23929951 | SRX19740074 | SRS17106148 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 017 5 dy post single ablation | GSM7085291 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation | 10X 22 017 5 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation | GSM7085291 | GSM7085291: 10X 22 017 5 dy post single ablation; Danio rerio; RNA Seq | GSM7085291 r1 | GSM7085291 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2004_S4_L002_R1_001.fastq.gz P25452_2004_S4_L002_R2_001.fastq.gz | fastq fastq | 13492044952.0 | 114339364.0 | GSM7085291 r1 | 0:28 1:90 | A:3873940551;C:2926902171;G:3135095393;T:3555720987;N:385850 | 28 | 90 | 3873940551 | 2926902171 | 3135095393 | 3555720987 | 385850 | SRX19740074 | SRS17106148 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00505 | 0.91196 | 0.00151 | 0.10926 | 0.99172 | 0.74633 | 0.3125 | 0.50464 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74428 | 74428 | SRR23929952 | SRX19740074 | SRS17106148 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 017 5 dy post single ablation | GSM7085291 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation | 10X 22 017 5 dy post single ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation | GSM7085291 | GSM7085291: 10X 22 017 5 dy post single ablation; Danio rerio; RNA Seq | GSM7085291 r1 | GSM7085291 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2004_S4_L001_R1_001.fastq.gz P25452_2004_S4_L001_R2_001.fastq.gz | fastq fastq | 13406231340.0 | 113612130.0 | GSM7085291 r2 | 0:28 1:90 | A:3850846331;C:2906712145;G:3113344227;T:3534865936;N:462701 | 28 | 90 | 3850846331 | 2906712145 | 3113344227 | 3534865936 | 462701 | SRX19740074 | SRS17106148 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00522 | 0.91073 | 0.00161 | 0.11013 | 0.99172 | 0.74665 | 0.2884 | 0.52618 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74429 | 74429 | SRR23929953 | SRX19740073 | SRS17106147 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 016 5 dy post double ablation | GSM7085290 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation | 10X 22 016 5 dy post double ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation | GSM7085290 | GSM7085290: 10X 22 016 5 dy post double ablation; Danio rerio; RNA Seq | GSM7085290 r1 | GSM7085290 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2003_S3_L002_R1_001.fastq.gz P25452_2003_S3_L002_R2_001.fastq.gz | fastq fastq | 29520641622.0 | 250174929.0 | GSM7085290 r1 | 0:28 1:90 | A:8496409320;C:6362210704;G:6766268604;T:7894905763;N:847231 | 28 | 90 | 8496409320 | 6362210704 | 6766268604 | 7894905763 | 847231 | SRX19740073 | SRS17106147 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00483 | 0.91059 | 0.00152 | 0.09736 | 0.99362 | 0.81937 | 0.31545 | 0.52536 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74430 | 74430 | SRR23929954 | SRX19740073 | SRS17106147 | SRP428435 | PRJNA941866 | Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish | GSE226841 | Transcriptome Analysis | The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry we used FACS to sort out mCherry positive cells in adult zebrafish pancreas indicating cells in the krt4+ cell lineage | pubmed:37595046 | 10X 22 016 5 dy post double ablation | GSM7085290 | source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation | 10X 22 016 5 dy post double ablation | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘ expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files | krt4 lineage traced cells in adult zebrafish pancreas | We selected 6 mpf 9 mpf fish with 8 10 fish in each condition We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS no calcium no magnesium for 10 minutes. Next we used blunt forceps to carefully remove the skin kidney eggs in females liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then we cut at the anterior region of the intestinal bulb and hindgut and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile we also removed the spleen appearing in dark red which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant we washed the pellets with 300 μL pre cooled solution containing 1% BSA 0.1% Pluronic F 68 and 0.1% DAPI and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS we selected single cell populations based on forward scatter and side scatter signals. Next we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension. | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation | GSM7085290 | GSM7085290: 10X 22 016 5 dy post double ablation; Danio rerio; RNA Seq | GSM7085290 r1 | GSM7085290 | 1 | Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles pooled denatured and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP428435 | loader:fastq load.py | P25452_2003_S3_L001_R1_001.fastq.gz P25452_2003_S3_L001_R2_001.fastq.gz | fastq fastq | 29361448176.0 | 248825832.0 | GSM7085290 r2 | 0:28 1:90 | A:8453733104;C:6324569877;G:6726263046;T:7855861357;N:1020792 | 28 | 90 | 8453733104 | 6324569877 | 6726263046 | 7855861357 | 1020792 | SRX19740073 | SRS17106147 | SRA1608504 | Karolinska Institute | Karolinska Institute | 2 | 0.00488 | 0.91294 | 0.00158 | 0.09794 | 0.99306 | 0.8182 | 0.31803 | 0.52363 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Sweden | 2023-03-07 | Adult | Adult | Pancreas | Endocrine System | ||||||||||
| 74472 | 74472 | SRR23824316 | SRX19646193 | SRS17014002 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 2 | GSM7092957 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092957 | GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq | GSM7092957 r1 | GSM7092957 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-2_S8_L001_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L001_R1_001.fastq.gz | fastq fastq | 4689094030.0 | 39738085.0 | GSM7092957 r1 | 0:28 1:90 | A:1232747701;C:1087501739;G:1176854549;T:1191883874;N:106167 | 28 | 90 | 1232747701 | 1087501739 | 1176854549 | 1191883874 | 106167 | SRX19646193 | SRS17014002 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00515 | 0.93252 | 0.00155 | 0.06137 | 0.99648 | 0.88692 | 0.38705 | 0.60914 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74473 | 74473 | SRR23824317 | SRX19646193 | SRS17014002 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 2 | GSM7092957 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092957 | GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq | GSM7092957 r1 | GSM7092957 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-2_S8_L002_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L002_R1_001.fastq.gz | fastq fastq | 4677907984.0 | 39643288.0 | GSM7092957 r2 | 0:28 1:90 | A:1227626448;C:1085304810;G:1174779891;T:1190095936;N:100899 | 28 | 90 | 1227626448 | 1085304810 | 1174779891 | 1190095936 | 100899 | SRX19646193 | SRS17014002 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00531 | 0.93306 | 0.00158 | 0.06221 | 0.99596 | 0.88749 | 0.37673 | 0.60528 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74474 | 74474 | SRR23824318 | SRX19646193 | SRS17014002 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 2 | GSM7092957 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092957 | GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq | GSM7092957 r1 | GSM7092957 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-2_S8_L003_R1_001.fastq.gz Ctrl-Pancreas-2_S8_L003_R2_001.fastq.gz | fastq fastq | 4761421422.0 | 40351029.0 | GSM7092957 r3 | 0:28 1:90 | A:1250348494;C:1104936433;G:1195812813;T:1210226243;N:97439 | 28 | 90 | 1250348494 | 1104936433 | 1195812813 | 1210226243 | 97439 | SRX19646193 | SRS17014002 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00518 | 0.93314 | 0.00149 | 0.06284 | 0.99596 | 0.88753 | 0.3933 | 0.60442 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74475 | 74475 | SRR23824319 | SRX19646193 | SRS17014002 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 2 | GSM7092957 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092957 | GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq | GSM7092957 r1 | GSM7092957 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-2_S8_L004_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L004_R1_001.fastq.gz | fastq fastq | 4667970850.0 | 39559075.0 | GSM7092957 r4 | 0:28 1:90 | A:1226515454;C:1082416982;G:1171222300;T:1187726852;N:89262 | 28 | 90 | 1226515454 | 1082416982 | 1171222300 | 1187726852 | 89262 | SRX19646193 | SRS17014002 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00499 | 0.93259 | 0.00167 | 0.0614 | 0.9959 | 0.88755 | 0.38604 | 0.53191 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74476 | 74476 | SRR23824320 | SRX19646192 | SRS17014003 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 1 | GSM7092956 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092956 | GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq | GSM7092956 r1 | GSM7092956 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-1_S4_L001_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L001_R2_001.fastq.gz | fastq fastq | 4087782314.0 | 34642223.0 | GSM7092956 r1 | 0:28 1:90 | A:988379101;C:980631744;G:1075271505;T:1043407296;N:92668 | 28 | 90 | 988379101 | 980631744 | 1075271505 | 1043407296 | 92668 | SRX19646192 | SRS17014003 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00484 | 0.96438 | 0.00131 | 0.03915 | 0.99697 | 0.91311 | 0.4152 | 0.60907 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74477 | 74477 | SRR23824321 | SRX19646192 | SRS17014003 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 1 | GSM7092956 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092956 | GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq | GSM7092956 r1 | GSM7092956 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-1_S4_L002_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L002_R2_001.fastq.gz | fastq fastq | 4117642214.0 | 34895273.0 | GSM7092956 r2 | 0:28 1:90 | A:995176406;C:987675179;G:1083314338;T:1051387356;N:88935 | 28 | 90 | 995176406 | 987675179 | 1083314338 | 1051387356 | 88935 | SRX19646192 | SRS17014003 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.0049 | 0.96448 | 0.00126 | 0.03869 | 0.99655 | 0.91151 | 0.42291 | 0.61172 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74478 | 74478 | SRR23824322 | SRX19646192 | SRS17014003 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 1 | GSM7092956 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092956 | GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq | GSM7092956 r1 | GSM7092956 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-1_S4_L003_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L003_R2_001.fastq.gz | fastq fastq | 4158634470.0 | 35242665.0 | GSM7092956 r3 | 0:28 1:90 | A:1004519785;C:998011643;G:1094510237;T:1061510107;N:82698 | 28 | 90 | 1004519785 | 998011643 | 1094510237 | 1061510107 | 82698 | SRX19646192 | SRS17014003 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00486 | 0.96439 | 0.00124 | 0.04007 | 0.99689 | 0.91064 | 0.40883 | 0.61125 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74479 | 74479 | SRR23824323 | SRX19646192 | SRS17014003 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas Ctrl replicate 1 | GSM7092956 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas Ctrl replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092956 | GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq | GSM7092956 r1 | GSM7092956 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | Ctrl-Pancreas-1_S4_L004_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L004_R2_001.fastq.gz | fastq fastq | 4084344502.0 | 34613089.0 | GSM7092956 r4 | 0:28 1:90 | A:988069108;C:979213026;G:1073790783;T:1043193951;N:77634 | 28 | 90 | 988069108 | 979213026 | 1073790783 | 1043193951 | 77634 | SRX19646192 | SRS17014003 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00479 | 0.96445 | 0.00132 | 0.0387 | 0.99701 | 0.91086 | 0.42113 | 0.61441 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74504 | 74504 | SRR23824344 | SRX19646185 | SRS17013995 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 1 | GSM7092948 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092948 | GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq | GSM7092948 r1 | GSM7092948 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-1_S20_L001_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L001_R2_001.fastq.gz | fastq fastq | 4549683756.0 | 38556642.0 | GSM7092948 r1 | 0:28 1:90 | A:1143775236;C:1105204092;G:1203189006;T:1097413006;N:102416 | 28 | 90 | 1143775236 | 1105204092 | 1203189006 | 1097413006 | 102416 | SRX19646185 | SRS17013995 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.02063 | 0.94539 | 0.00665 | 0.10755 | 0.99622 | 0.91309 | 0.32854 | 0.54953 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74505 | 74505 | SRR23824345 | SRX19646185 | SRS17013995 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 1 | GSM7092948 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092948 | GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq | GSM7092948 r1 | GSM7092948 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-1_S20_L002_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L002_R2_001.fastq.gz | fastq fastq | 4517687938.0 | 38285491.0 | GSM7092948 r2 | 0:28 1:90 | A:1134622351;C:1097536764;G:1194906587;T:1090524287;N:97949 | 28 | 90 | 1134622351 | 1097536764 | 1194906587 | 1090524287 | 97949 | SRX19646185 | SRS17013995 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.02109 | 0.94517 | 0.00676 | 0.10863 | 0.99628 | 0.91252 | 0.3052 | 0.54958 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74506 | 74506 | SRR23824346 | SRX19646185 | SRS17013995 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 1 | GSM7092948 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092948 | GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq | GSM7092948 r1 | GSM7092948 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-1_S20_L003_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L003_R2_001.fastq.gz | fastq fastq | 4636317940.0 | 39290830.0 | GSM7092948 r3 | 0:28 1:90 | A:1163890164;C:1127297116;G:1227016473;T:1118019811;N:94376 | 28 | 90 | 1163890164 | 1127297116 | 1227016473 | 1118019811 | 94376 | SRX19646185 | SRS17013995 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.02099 | 0.94599 | 0.00695 | 0.10973 | 0.99618 | 0.9123 | 0.34518 | 0.51887 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74507 | 74507 | SRR23824347 | SRX19646185 | SRS17013995 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 1 | GSM7092948 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092948 | GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq | GSM7092948 r1 | GSM7092948 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-1_S20_L004_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L004_R2_001.fastq.gz | fastq fastq | 4497198064.0 | 38111848.0 | GSM7092948 r4 | 0:28 1:90 | A:1131098871;C:1091572129;G:1188115242;T:1086325472;N:86350 | 28 | 90 | 1131098871 | 1091572129 | 1188115242 | 1086325472 | 86350 | SRX19646185 | SRS17013995 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.02003 | 0.9465 | 0.00658 | 0.10877 | 0.99596 | 0.91171 | 0.34392 | 0.54247 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74508 | 74508 | SRR23824348 | SRX19646184 | SRS17013994 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 2 | GSM7092949 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092949 | GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq | GSM7092949 r1 | GSM7092949 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-2_S24_L001_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L001_R2_001.fastq.gz | fastq fastq | 3694404180.0 | 31308510.0 | GSM7092949 r1 | 0:28 1:90 | A:925642312;C:897963126;G:972697543;T:898017524;N:83675 | 28 | 90 | 925642312 | 897963126 | 972697543 | 898017524 | 83675 | SRX19646184 | SRS17013994 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.01944 | 0.9386 | 0.00639 | 0.10031 | 0.99561 | 0.90763 | 0.34147 | 0.64485 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74509 | 74509 | SRR23824349 | SRX19646184 | SRS17013994 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 2 | GSM7092949 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092949 | GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq | GSM7092949 r1 | GSM7092949 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-2_S24_L002_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L002_R2_001.fastq.gz | fastq fastq | 3695460280.0 | 31317460.0 | GSM7092949 r2 | 0:28 1:90 | A:924776645;C:898527265;G:973466829;T:898610296;N:79245 | 28 | 90 | 924776645 | 898527265 | 973466829 | 898610296 | 79245 | SRX19646184 | SRS17013994 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.01959 | 0.93749 | 0.00645 | 0.10075 | 0.99571 | 0.90889 | 0.36214 | 0.64826 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74510 | 74510 | SRR23824350 | SRX19646184 | SRS17013994 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 2 | GSM7092949 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092949 | GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq | GSM7092949 r1 | GSM7092949 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-2_S24_L003_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L003_R2_001.fastq.gz | fastq fastq | 3765831586.0 | 31913827.0 | GSM7092949 r3 | 0:28 1:90 | A:942337142;C:916041305;G:992299130;T:915077569;N:76440 | 28 | 90 | 942337142 | 916041305 | 992299130 | 915077569 | 76440 | SRX19646184 | SRS17013994 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.0193 | 0.93865 | 0.00649 | 0.1012 | 0.99614 | 0.9093 | 0.34282 | 0.63758 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74511 | 74511 | SRR23824351 | SRX19646184 | SRS17013994 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 7 dpi replicate 2 | GSM7092949 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 7 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092949 | GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq | GSM7092949 r1 | GSM7092949 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 7dpi-Pancreas-2_S24_L004_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L004_R2_001.fastq.gz | fastq fastq | 3665890896.0 | 31066872.0 | GSM7092949 r4 | 0:28 1:90 | A:918497729;C:890554002;G:964737735;T:892032221;N:69209 | 28 | 90 | 918497729 | 890554002 | 964737735 | 892032221 | 69209 | SRX19646184 | SRS17013994 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.01901 | 0.93844 | 0.0062 | 0.10108 | 0.99592 | 0.90796 | 0.32691 | 0.64748 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74544 | 74544 | SRR23824380 | SRX19646175 | SRS17013985 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 2 | GSM7092941 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092941 | GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq | GSM7092941 r1 | GSM7092941 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-2_S16_L001_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L001_R2_001.fastq.gz | fastq fastq | 4309260644.0 | 36519158.0 | GSM7092941 r1 | 0:28 1:90 | A:1046247537;C:1048122611;G:1162975668;T:1051816689;N:98139 | 28 | 90 | 1046247537 | 1048122611 | 1162975668 | 1051816689 | 98139 | SRX19646175 | SRS17013985 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00671 | 0.9366 | 0.00224 | 0.09388 | 0.99651 | 0.90189 | 0.37644 | 0.63945 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74545 | 74545 | SRR23824381 | SRX19646175 | SRS17013985 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 2 | GSM7092941 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092941 | GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq | GSM7092941 r1 | GSM7092941 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-2_S16_L002_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L002_R2_001.fastq.gz | fastq fastq | 4297639414.0 | 36420673.0 | GSM7092941 r2 | 0:28 1:90 | A:1043016765;C:1045256212;G:1159666945;T:1049606913;N:92579 | 28 | 90 | 1043016765 | 1045256212 | 1159666945 | 1049606913 | 92579 | SRX19646175 | SRS17013985 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00646 | 0.93715 | 0.00204 | 0.09343 | 0.99685 | 0.90327 | 0.38255 | 0.63012 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74546 | 74546 | SRR23824382 | SRX19646175 | SRS17013985 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 2 | GSM7092941 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092941 | GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq | GSM7092941 r1 | GSM7092941 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-2_S16_L003_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L003_R2_001.fastq.gz | fastq fastq | 4389542888.0 | 37199516.0 | GSM7092941 r3 | 0:28 1:90 | A:1064162384;C:1068512248;G:1185538637;T:1071241453;N:88166 | 28 | 90 | 1064162384 | 1068512248 | 1185538637 | 1071241453 | 88166 | SRX19646175 | SRS17013985 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00644 | 0.93752 | 0.0021 | 0.09439 | 0.99659 | 0.90382 | 0.37098 | 0.63183 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74547 | 74547 | SRR23824383 | SRX19646175 | SRS17013985 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 2 | GSM7092941 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 2 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092941 | GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq | GSM7092941 r1 | GSM7092941 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-2_S16_L004_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L004_R2_001.fastq.gz | fastq fastq | 4277274856.0 | 36248092.0 | GSM7092941 r4 | 0:28 1:90 | A:1039365242;C:1039483839;G:1153145758;T:1045198402;N:81615 | 28 | 90 | 1039365242 | 1039483839 | 1153145758 | 1045198402 | 81615 | SRX19646175 | SRS17013985 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00627 | 0.93724 | 0.00211 | 0.09386 | 0.99659 | 0.90262 | 0.4275 | 0.61845 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74548 | 74548 | SRR23824388 | SRX19646174 | SRS17013984 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 1 | GSM7092940 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092940 | GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq | GSM7092940 r1 | GSM7092940 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-1_S12_L001_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L001_R2_001.fastq.gz | fastq fastq | 5429558190.0 | 46013205.0 | GSM7092940 r1 | 0:28 1:90 | A:1303586809;C:1328725175;G:1505666398;T:1291455764;N:124044 | 28 | 90 | 1303586809 | 1328725175 | 1505666398 | 1291455764 | 124044 | SRX19646174 | SRS17013984 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00632 | 0.94424 | 0.00213 | 0.10919 | 0.99695 | 0.91936 | 0.36162 | 0.55183 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74549 | 74549 | SRR23824389 | SRX19646174 | SRS17013984 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 1 | GSM7092940 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092940 | GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq | GSM7092940 r1 | GSM7092940 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-1_S12_L002_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L002_R2_001.fastq.gz | fastq fastq | 5406650142.0 | 45819069.0 | GSM7092940 r2 | 0:28 1:90 | A:1297924443;C:1322864150;G:1498812275;T:1286932180;N:117094 | 28 | 90 | 1297924443 | 1322864150 | 1498812275 | 1286932180 | 117094 | SRX19646174 | SRS17013984 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00647 | 0.94374 | 0.00235 | 0.11112 | 0.99699 | 0.91816 | 0.3583 | 0.56118 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74550 | 74550 | SRR23824390 | SRX19646174 | SRS17013984 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 1 | GSM7092940 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092940 | GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq | GSM7092940 r1 | GSM7092940 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-1_S12_L003_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L003_R2_001.fastq.gz | fastq fastq | 5529750810.0 | 46862295.0 | GSM7092940 r3 | 0:28 1:90 | A:1325091638;C:1354598961;G:1534908275;T:1315039358;N:112578 | 28 | 90 | 1325091638 | 1354598961 | 1534908275 | 1315039358 | 112578 | SRX19646174 | SRS17013984 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00611 | 0.94576 | 0.00203 | 0.11108 | 0.99709 | 0.91863 | 0.38685 | 0.65557 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 74551 | 74551 | SRR23824391 | SRX19646174 | SRS17013984 | SRP426909 | PRJNA943553 | Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] | GSE227190 | Transcriptome Analysis | Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls. | parent bioproject:PRJNA943547 | pubmed:39627536 | Pancreas 1 dpi replicate 1 | GSM7092940 | source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | Pancreas 1 dpi replicate 1 | Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format. | Pancreas | Heart cryoinjury or untreated | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | Standard zebrafish husbandry protocol. | tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury | GSM7092940 | GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq | GSM7092940 r1 | GSM7092940 | 1 | Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai… | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP426909 | loader:fastq load.py | 1dpi-Pancreas-1_S12_L004_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L004_R2_001.fastq.gz | fastq fastq | 5383384318.0 | 45621901.0 | GSM7092940 r4 | 0:28 1:90 | A:1294350602;C:1316150189;G:1490887301;T:1281893201;N:103025 | 28 | 90 | 1294350602 | 1316150189 | 1490887301 | 1281893201 | 103025 | SRX19646174 | SRS17013984 | SRA1603354 | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine | 2 | 0.00616 | 0.94398 | 0.00206 | 0.10993 | 0.99715 | 0.91963 | 0.37232 | 0.65892 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-12 | Undetermined | Undetermined | Pancreas | Endocrine System | ||||||||
| 76740 | 76740 | SRR25374386 | SRX21113512 | SRS18382106 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 A10 | GSM7655684 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 A10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655684 | GSM7655684: ExVi2Red 01 A10; Danio rerio; RNA Seq | GSM7655684 r1 | GSM7655684 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21286_Track-51602_R1.fastq.gz | fastq | 38304684.0 | 504009.0 | GSM7655684 r1 | 0:76 | A:10444153;C:8397210;G:8505443;T:10956830;N:1048 | 76 | 10444153 | 8397210 | 8505443 | 10956830 | 1048 | SRX21113512 | SRS18382106 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.78167 | 0.12085 | 0.94621 | 0.44883 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76741 | 76741 | SRR25374387 | SRX21113511 | SRS18382105 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 B10 | GSM7655683 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 B10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655683 | GSM7655683: ExVi2Red 01 B10; Danio rerio; RNA Seq | GSM7655683 r1 | GSM7655683 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21287_Track-51603_R1.fastq.gz | fastq | 41818544.0 | 550244.0 | GSM7655683 r1 | 0:76 | A:11263718;C:9415229;G:9551199;T:11587507;N:891 | 76 | 11263718 | 9415229 | 9551199 | 11587507 | 891 | SRX21113511 | SRS18382105 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.72269 | 0.12564 | 0.9542 | 0.55822 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76742 | 76742 | SRR25374388 | SRX21113510 | SRS18382104 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 C10 | GSM7655682 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 C10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655682 | GSM7655682: ExVi2Red 01 C10; Danio rerio; RNA Seq | GSM7655682 r1 | GSM7655682 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21288_Track-51604_R1.fastq.gz | fastq | 41119648.0 | 541048.0 | GSM7655682 r1 | 0:76 | A:10732270;C:9662921;G:9639944;T:11083600;N:913 | 76 | 10732270 | 9662921 | 9639944 | 11083600 | 913 | SRX21113510 | SRS18382104 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.86963 | 0.06809 | 0.93292 | 0.65489 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76743 | 76743 | SRR25374389 | SRX21113509 | SRS18382103 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 D10 | GSM7655681 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 D10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655681 | GSM7655681: ExVi2Red 01 D10; Danio rerio; RNA Seq | GSM7655681 r1 | GSM7655681 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21289_Track-51605_R1.fastq.gz | fastq | 42475108.0 | 558883.0 | GSM7655681 r1 | 0:76 | A:11042198;C:9997401;G:9991867;T:11442635;N:1007 | 76 | 11042198 | 9997401 | 9991867 | 11442635 | 1007 | SRX21113509 | SRS18382103 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.85259 | 0.05736 | 0.94223 | 0.68549 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76744 | 76744 | SRR25374390 | SRX21113508 | SRS18382102 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 E10 | GSM7655680 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 E10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655680 | GSM7655680: ExVi2Red 01 E10; Danio rerio; RNA Seq | GSM7655680 r1 | GSM7655680 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21290_Track-51606_R1.fastq.gz | fastq | 42190564.0 | 555139.0 | GSM7655680 r1 | 0:76 | A:10880720;C:9985936;G:9919117;T:11403588;N:1203 | 76 | 10880720 | 9985936 | 9919117 | 11403588 | 1203 | SRX21113508 | SRS18382102 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84883 | 0.06243 | 0.94387 | 0.71713 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76745 | 76745 | SRR25374391 | SRX21113507 | SRS18382101 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 F10 | GSM7655679 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 F10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655679 | GSM7655679: ExVi2Red 01 F10; Danio rerio; RNA Seq | GSM7655679 r1 | GSM7655679 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21291_Track-51607_R1.fastq.gz | fastq | 30276196.0 | 398371.0 | GSM7655679 r1 | 0:76 | A:7966868;C:7016730;G:7000707;T:8291155;N:736 | 76 | 7966868 | 7016730 | 7000707 | 8291155 | 736 | SRX21113507 | SRS18382101 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.83303 | 0.05427 | 0.93785 | 0.69443 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76746 | 76746 | SRR25374392 | SRX21113506 | SRS18382100 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 G10 | GSM7655678 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 G10 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655678 | GSM7655678: ExVi2Red 01 G10; Danio rerio; RNA Seq | GSM7655678 r1 | GSM7655678 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21292_Track-51608_R1.fastq.gz | fastq | 42697028.0 | 561803.0 | GSM7655678 r1 | 0:76 | A:11421256;C:9416456;G:9762806;T:12095440;N:1070 | 76 | 11421256 | 9416456 | 9762806 | 12095440 | 1070 | SRX21113506 | SRS18382100 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.4772 | 0.03926 | 0.94742 | 0.64918 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76747 | 76747 | SRR25374393 | SRX21113505 | SRS18382099 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 H01 | GSM7655653 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 H01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655653 | GSM7655653: ExVi16Gr 02 H01; Danio rerio; RNA Seq | GSM7655653 r1 | GSM7655653 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21317_Track-51633_R1.fastq.gz | fastq | 39867624.0 | 524574.0 | GSM7655653 r1 | 0:76 | A:10664168;C:9072852;G:9105099;T:11024563;N:942 | 76 | 10664168 | 9072852 | 9105099 | 11024563 | 942 | SRX21113505 | SRS18382099 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.83797 | 0.06671 | 0.94044 | 0.62345 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76748 | 76748 | SRR25374394 | SRX21113504 | SRS18382098 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 A02 | GSM7655652 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 A02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655652 | GSM7655652: ExVi16Gr 02 A02; Danio rerio; RNA Seq | GSM7655652 r1 | GSM7655652 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21318_Track-51634_R1.fastq.gz | fastq | 37836752.0 | 497852.0 | GSM7655652 r1 | 0:76 | A:10538160;C:8088084;G:8235430;T:10974153;N:925 | 76 | 10538160 | 8088084 | 8235430 | 10974153 | 925 | SRX21113504 | SRS18382098 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.80039 | 0.2249 | 0.95392 | 0.68704 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76749 | 76749 | SRR25374395 | SRX21113503 | SRS18382097 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 B02 | GSM7655651 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 B02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655651 | GSM7655651: ExVi16Gr 02 B02; Danio rerio; RNA Seq | GSM7655651 r1 | GSM7655651 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21319_Track-51635_R1.fastq.gz | fastq | 37765464.0 | 496914.0 | GSM7655651 r1 | 0:76 | A:10327605;C:8440804;G:8513957;T:10482149;N:949 | 76 | 10327605 | 8440804 | 8513957 | 10482149 | 949 | SRX21113503 | SRS18382097 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.79171 | 0.10658 | 0.93785 | 0.57458 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76750 | 76750 | SRR25374396 | SRX21113502 | SRS18382096 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 C02 | GSM7655650 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 C02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655650 | GSM7655650: ExVi16Gr 02 C02; Danio rerio; RNA Seq | GSM7655650 r1 | GSM7655650 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21320_Track-51636_R1.fastq.gz | fastq | 33616016.0 | 442316.0 | GSM7655650 r1 | 0:76 | A:9130691;C:7426220;G:7511228;T:9547023;N:854 | 76 | 9130691 | 7426220 | 7511228 | 9547023 | 854 | SRX21113502 | SRS18382096 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.8161 | 0.16087 | 0.94282 | 0.74593 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76751 | 76751 | SRR25374397 | SRX21113501 | SRS18382094 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 D02 | GSM7655649 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 D02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655649 | GSM7655649: ExVi16Gr 02 D02; Danio rerio; RNA Seq | GSM7655649 r1 | GSM7655649 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21321_Track-51637_R1.fastq.gz | fastq | 48530712.0 | 638562.0 | GSM7655649 r1 | 0:76 | A:12706296;C:11286685;G:11268611;T:13267981;N:1139 | 76 | 12706296 | 11286685 | 11268611 | 13267981 | 1139 | SRX21113501 | SRS18382094 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.87539 | 0.05636 | 0.94509 | 0.67319 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76752 | 76752 | SRR25374398 | SRX21113500 | SRS18382095 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 E02 | GSM7655648 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 E02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655648 | GSM7655648: ExVi16Gr 02 E02; Danio rerio; RNA Seq | GSM7655648 r1 | GSM7655648 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21322_Track-51638_R1.fastq.gz | fastq | 38063080.0 | 500830.0 | GSM7655648 r1 | 0:76 | A:10345224;C:8528904;G:8613676;T:10574273;N:1003 | 76 | 10345224 | 8528904 | 8613676 | 10574273 | 1003 | SRX21113500 | SRS18382095 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.82962 | 0.12581 | 0.94334 | 0.5417 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76753 | 76753 | SRR25374399 | SRX21113499 | SRS18382093 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 F02 | GSM7655647 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 F02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655647 | GSM7655647: ExVi16Gr 02 F02; Danio rerio; RNA Seq | GSM7655647 r1 | GSM7655647 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21323_Track-51639_R1.fastq.gz | fastq | 33778504.0 | 444454.0 | GSM7655647 r1 | 0:76 | A:8715964;C:7998179;G:7952604;T:9110906;N:851 | 76 | 8715964 | 7998179 | 7952604 | 9110906 | 851 | SRX21113499 | SRS18382093 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.86888 | 0.04769 | 0.9417 | 0.71664 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76754 | 76754 | SRR25374400 | SRX21113498 | SRS18382091 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 G02 | GSM7655646 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 G02 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655646 | GSM7655646: ExVi16Gr 02 G02; Danio rerio; RNA Seq | GSM7655646 r1 | GSM7655646 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21324_Track-51640_R1.fastq.gz | fastq | 38434264.0 | 505714.0 | GSM7655646 r1 | 0:76 | A:10173498;C:8859852;G:8871249;T:10528740;N:925 | 76 | 10173498 | 8859852 | 8871249 | 10528740 | 925 | SRX21113498 | SRS18382091 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84613 | 0.07553 | 0.93839 | 0.68257 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76755 | 76755 | SRR25374401 | SRX21113497 | SRS18382092 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 H04 | GSM7655629 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 H04 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655629 | GSM7655629: ExVi16Gr 02 H04; Danio rerio; RNA Seq | GSM7655629 r1 | GSM7655629 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21341_Track-51657_R1.fastq.gz | fastq | 30968860.0 | 407485.0 | GSM7655629 r1 | 0:76 | A:8289373;C:7104056;G:7130406;T:8444292;N:733 | 76 | 8289373 | 7104056 | 7130406 | 8444292 | 733 | SRX21113497 | SRS18382092 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.89416 | 0.07736 | 0.9217 | 0.52336 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76756 | 76756 | SRR25374402 | SRX21113496 | SRS18382090 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 A05 | GSM7655628 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 A05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655628 | GSM7655628: ExVi16Gr 02 A05; Danio rerio; RNA Seq | GSM7655628 r1 | GSM7655628 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21342_Track-51658_R1.fastq.gz | fastq | 77775132.0 | 1023357.0 | GSM7655628 r1 | 0:76 | A:20285912;C:17896974;G:18105934;T:21484315;N:1997 | 76 | 20285912 | 17896974 | 18105934 | 21484315 | 1997 | SRX21113496 | SRS18382090 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.85173 | 0.08581 | 0.94923 | 0.6598 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76757 | 76757 | SRR25374403 | SRX21113495 | SRS18382089 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 B05 | GSM7655627 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 B05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655627 | GSM7655627: ExVi16Gr 02 B05; Danio rerio; RNA Seq | GSM7655627 r1 | GSM7655627 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21343_Track-51659_R1.fastq.gz | fastq | 48071824.0 | 632524.0 | GSM7655627 r1 | 0:76 | A:13026880;C:10835674;G:10943843;T:13264257;N:1170 | 76 | 13026880 | 10835674 | 10943843 | 13264257 | 1170 | SRX21113495 | SRS18382089 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.8831 | 0.07207 | 0.91881 | 0.53229 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76758 | 76758 | SRR25374404 | SRX21113494 | SRS18382088 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 C05 | GSM7655626 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 C05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655626 | GSM7655626: ExVi16Gr 02 C05; Danio rerio; RNA Seq | GSM7655626 r1 | GSM7655626 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21344_Track-51660_R1.fastq.gz | fastq | 44401404.0 | 584229.0 | GSM7655626 r1 | 0:76 | A:11837676;C:10159931;G:10224645;T:12177927;N:1225 | 76 | 11837676 | 10159931 | 10224645 | 12177927 | 1225 | SRX21113494 | SRS18382088 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.8662 | 0.10475 | 0.93939 | 0.61495 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76759 | 76759 | SRR25374405 | SRX21113493 | SRS18382087 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 D05 | GSM7655625 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 D05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655625 | GSM7655625: ExVi16Gr 02 D05; Danio rerio; RNA Seq | GSM7655625 r1 | GSM7655625 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21345_Track-51661_R1.fastq.gz | fastq | 40097980.0 | 527605.0 | GSM7655625 r1 | 0:76 | A:10996482;C:8953433;G:9037603;T:11109378;N:1084 | 76 | 10996482 | 8953433 | 9037603 | 11109378 | 1084 | SRX21113493 | SRS18382087 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.8426 | 0.13642 | 0.94245 | 0.59961 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76760 | 76760 | SRR25374406 | SRX21113492 | SRS18382086 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | UHR 02 E05 | GSM7655624 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | UHR 02 E05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655624 | GSM7655624: UHR 02 E05; Danio rerio; RNA Seq | GSM7655624 r1 | GSM7655624 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21346_Track-51662_R1.fastq.gz | fastq | 73001572.0 | 960547.0 | GSM7655624 r1 | 0:76 | A:18801430;C:17125045;G:17615098;T:19458134;N:1865 | 76 | 18801430 | 17125045 | 17615098 | 19458134 | 1865 | SRX21113492 | SRS18382086 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.00277 | 0.00188 | 0.99906 | 0.73509 | 76 | T | under 1.2% mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76761 | 76761 | SRR25374407 | SRX21113491 | SRS18382085 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 F05 | GSM7655623 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 F05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655623 | GSM7655623: ExVi16Gr 02 F05; Danio rerio; RNA Seq | GSM7655623 r1 | GSM7655623 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21347_Track-51663_R1.fastq.gz | fastq | 27670764.0 | 364089.0 | GSM7655623 r1 | 0:76 | A:7066830;C:6632931;G:6548167;T:7422248;N:588 | 76 | 7066830 | 6632931 | 6548167 | 7422248 | 588 | SRX21113491 | SRS18382085 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.87564 | 0.03905 | 0.92614 | 0.74611 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76762 | 76762 | SRR25374408 | SRX21113490 | SRS18382083 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 G05 | GSM7655622 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 G05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655622 | GSM7655622: ExVi16Gr 02 G05; Danio rerio; RNA Seq | GSM7655622 r1 | GSM7655622 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21348_Track-51664_R1.fastq.gz | fastq | 42969260.0 | 565385.0 | GSM7655622 r1 | 0:76 | A:11590827;C:9713842;G:9805929;T:11857589;N:1073 | 76 | 11590827 | 9713842 | 9805929 | 11857589 | 1073 | SRX21113490 | SRS18382083 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84464 | 0.11633 | 0.94939 | 0.6516 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76763 | 76763 | SRR25374409 | SRX21113489 | SRS18382084 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 H08 | GSM7655597 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 H08 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655597 | GSM7655597: ExVi16Gr 02 H08; Danio rerio; RNA Seq | GSM7655597 r1 | GSM7655597 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21373_Track-51689_R1.fastq.gz | fastq | 38007448.0 | 500098.0 | GSM7655597 r1 | 0:76 | A:10173426;C:8641625;G:8730744;T:10460660;N:993 | 76 | 10173426 | 8641625 | 8730744 | 10460660 | 993 | SRX21113489 | SRS18382084 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.79669 | 0.08276 | 0.95067 | 0.65876 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76764 | 76764 | SRR25374410 | SRX21113488 | SRS18382082 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 A09 | GSM7655596 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 A09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655596 | GSM7655596: ExVi16Gr 02 A09; Danio rerio; RNA Seq | GSM7655596 r1 | GSM7655596 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21374_Track-51690_R1.fastq.gz | fastq | 44346608.0 | 583508.0 | GSM7655596 r1 | 0:76 | A:11794284;C:10211396;G:10275551;T:12064327;N:1050 | 76 | 11794284 | 10211396 | 10275551 | 12064327 | 1050 | SRX21113488 | SRS18382082 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84786 | 0.10747 | 0.9432 | 0.64267 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76765 | 76765 | SRR25374411 | SRX21113487 | SRS18382081 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 B09 | GSM7655595 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 B09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655595 | GSM7655595: ExVi16Gr 02 B09; Danio rerio; RNA Seq | GSM7655595 r1 | GSM7655595 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21375_Track-51691_R1.fastq.gz | fastq | 43404512.0 | 571112.0 | GSM7655595 r1 | 0:76 | A:11406215;C:10089747;G:10096444;T:11811131;N:975 | 76 | 11406215 | 10089747 | 10096444 | 11811131 | 975 | SRX21113487 | SRS18382081 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.87723 | 0.08948 | 0.94365 | 0.60874 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76766 | 76766 | SRR25374412 | SRX21113486 | SRS18382080 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 C09 | GSM7655594 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 C09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655594 | GSM7655594: ExVi16Gr 02 C09; Danio rerio; RNA Seq | GSM7655594 r1 | GSM7655594 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21376_Track-51692_R1.fastq.gz | fastq | 45027036.0 | 592461.0 | GSM7655594 r1 | 0:76 | A:11841919;C:10492780;G:10537256;T:12153887;N:1194 | 76 | 11841919 | 10492780 | 10537256 | 12153887 | 1194 | SRX21113486 | SRS18382080 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84983 | 0.08729 | 0.93584 | 0.63209 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76767 | 76767 | SRR25374413 | SRX21113485 | SRS18382079 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 D09 | GSM7655593 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 D09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655593 | GSM7655593: ExVi16Gr 02 D09; Danio rerio; RNA Seq | GSM7655593 r1 | GSM7655593 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21377_Track-51693_R1.fastq.gz | fastq | 12382908.0 | 162933.0 | GSM7655593 r1 | 0:76 | A:3238636;C:2869308;G:2881983;T:3392821;N:160 | 76 | 3238636 | 2869308 | 2881983 | 3392821 | 160 | SRX21113485 | SRS18382079 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.83061 | 0.05654 | 0.94558 | 0.64901 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76768 | 76768 | SRR25374414 | SRX21113484 | SRS18382077 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 E09 | GSM7655592 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 E09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655592 | GSM7655592: ExVi16Gr 02 E09; Danio rerio; RNA Seq | GSM7655592 r1 | GSM7655592 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21378_Track-51694_R1.fastq.gz | fastq | 35251232.0 | 463832.0 | GSM7655592 r1 | 0:76 | A:9503812;C:8037895;G:8131353;T:9577315;N:857 | 76 | 9503812 | 8037895 | 8131353 | 9577315 | 857 | SRX21113484 | SRS18382077 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.77275 | 0.07657 | 0.94836 | 0.59607 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76769 | 76769 | SRR25374415 | SRX21113483 | SRS18382078 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 F09 | GSM7655591 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 F09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655591 | GSM7655591: ExVi16Gr 02 F09; Danio rerio; RNA Seq | GSM7655591 r1 | GSM7655591 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21379_Track-51695_R1.fastq.gz | fastq | 29051836.0 | 382261.0 | GSM7655591 r1 | 0:76 | A:7518130;C:6891176;G:6876887;T:7764943;N:700 | 76 | 7518130 | 6891176 | 6876887 | 7764943 | 700 | SRX21113483 | SRS18382078 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.86709 | 0.07623 | 0.94495 | 0.65172 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76770 | 76770 | SRR25374416 | SRX21113482 | SRS18382076 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi16Gr 02 G09 | GSM7655590 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi16Gr 02 G09 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655590 | GSM7655590: ExVi16Gr 02 G09; Danio rerio; RNA Seq | GSM7655590 r1 | GSM7655590 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21380_Track-51696_R1.fastq.gz | fastq | 109516.0 | 1441.0 | GSM7655590 r1 | 0:76 | A:29131;C:25838;G:25349;T:29198;N:0 | 76 | 29131 | 25838 | 25349 | 29198 | 0 | SRX21113482 | SRS18382076 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.76586 | 0.05934 | 0.99277 | 0.74208 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76771 | 76771 | SRR25374417 | SRX21113481 | SRS18382075 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 A01 | GSM7655755 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 A01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655755 | GSM7655755: ExVi2Red 01 A01; Danio rerio; RNA Seq | GSM7655755 r1 | GSM7655755 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21214_Track-51531_R1.fastq.gz | fastq | 45532968.0 | 599118.0 | GSM7655755 r1 | 0:76 | A:12246803;C:10349678;G:10361865;T:12573403;N:1219 | 76 | 12246803 | 10349678 | 10361865 | 12573403 | 1219 | SRX21113481 | SRS18382075 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.87285 | 0.0881 | 0.90136 | 0.6883 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76772 | 76772 | SRR25374418 | SRX21113480 | SRS18382074 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 B01 | GSM7655754 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 B01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655754 | GSM7655754: ExVi2Red 01 B01; Danio rerio; RNA Seq | GSM7655754 r1 | GSM7655754 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21215_Track-51532_R1.fastq.gz | fastq | 34996100.0 | 460475.0 | GSM7655754 r1 | 0:76 | A:9331462;C:8037189;G:8071185;T:9555393;N:871 | 76 | 9331462 | 8037189 | 8071185 | 9555393 | 871 | SRX21113480 | SRS18382074 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84607 | 0.05475 | 0.92374 | 0.60845 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76773 | 76773 | SRR25374419 | SRX21113479 | SRS18382073 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 C01 | GSM7655753 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 C01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655753 | GSM7655753: ExVi2Red 01 C01; Danio rerio; RNA Seq | GSM7655753 r1 | GSM7655753 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21216_Track-51533_R1.fastq.gz | fastq | 35915548.0 | 472573.0 | GSM7655753 r1 | 0:76 | A:9876241;C:7948709;G:8031565;T:10058067;N:966 | 76 | 9876241 | 7948709 | 8031565 | 10058067 | 966 | SRX21113479 | SRS18382073 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.83728 | 0.10675 | 0.94426 | 0.70513 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76774 | 76774 | SRR25374420 | SRX21113478 | SRS18382072 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 D01 | GSM7655752 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 D01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655752 | GSM7655752: ExVi2Red 01 D01; Danio rerio; RNA Seq | GSM7655752 r1 | GSM7655752 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21217_Track-51534_R1.fastq.gz | fastq | 40427896.0 | 531946.0 | GSM7655752 r1 | 0:76 | A:10795650;C:9203028;G:9208037;T:11220185;N:996 | 76 | 10795650 | 9203028 | 9208037 | 11220185 | 996 | SRX21113478 | SRS18382072 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.82317 | 0.05906 | 0.93229 | 0.65906 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76775 | 76775 | SRR25374421 | SRX21113477 | SRS18382071 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 E01 | GSM7655751 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 E01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655751 | GSM7655751: ExVi2Red 01 E01; Danio rerio; RNA Seq | GSM7655751 r1 | GSM7655751 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21218_Track-51535_R1.fastq.gz | fastq | 44180016.0 | 581316.0 | GSM7655751 r1 | 0:76 | A:11920819;C:10035364;G:10070579;T:12151996;N:1258 | 76 | 11920819 | 10035364 | 10070579 | 12151996 | 1258 | SRX21113477 | SRS18382071 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.87211 | 0.08161 | 0.9011 | 0.58341 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76776 | 76776 | SRR25374422 | SRX21113476 | SRS18382069 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 F01 | GSM7655750 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 F01 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655750 | GSM7655750: ExVi2Red 01 F01; Danio rerio; RNA Seq | GSM7655750 r1 | GSM7655750 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21219_Track-51536_R1.fastq.gz | fastq | 33634636.0 | 442561.0 | GSM7655750 r1 | 0:76 | A:8955856;C:7717906;G:7739888;T:9220366;N:620 | 76 | 8955856 | 7717906 | 7739888 | 9220366 | 620 | SRX21113476 | SRS18382069 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.79266 | 0.0799 | 0.93852 | 0.6609 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76777 | 76777 | SRR25374423 | SRX21113475 | SRS18382070 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 G04 | GSM7655725 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 G04 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655725 | GSM7655725: ExVi2Red 01 G04; Danio rerio; RNA Seq | GSM7655725 r1 | GSM7655725 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21244_Track-51561_R1.fastq.gz | fastq | 28279068.0 | 372093.0 | GSM7655725 r1 | 0:76 | A:7573141;C:6458500;G:6502179;T:7744670;N:578 | 76 | 7573141 | 6458500 | 6502179 | 7744670 | 578 | SRX21113475 | SRS18382070 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.82931 | 0.07538 | 0.93892 | 0.57086 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76778 | 76778 | SRR25374424 | SRX21113474 | SRS18382068 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 H04 | GSM7655724 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 H04 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655724 | GSM7655724: ExVi2Red 01 H04; Danio rerio; RNA Seq | GSM7655724 r1 | GSM7655724 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21245_Track-51562_R1.fastq.gz | fastq | 33646188.0 | 442713.0 | GSM7655724 r1 | 0:76 | A:8914312;C:7724087;G:7709961;T:9296909;N:919 | 76 | 8914312 | 7724087 | 7709961 | 9296909 | 919 | SRX21113474 | SRS18382068 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.83628 | 0.07615 | 0.94123 | 0.62167 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76779 | 76779 | SRR25374425 | SRX21113473 | SRS18382067 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 A05 | GSM7655723 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 A05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655723 | GSM7655723: ExVi2Red 01 A05; Danio rerio; RNA Seq | GSM7655723 r1 | GSM7655723 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21246_Track-51563_R1.fastq.gz | fastq | 65374820.0 | 860195.0 | GSM7655723 r1 | 0:76 | A:17920811;C:14416412;G:14755021;T:18280774;N:1802 | 76 | 17920811 | 14416412 | 14755021 | 18280774 | 1802 | SRX21113473 | SRS18382067 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.82654 | 0.12154 | 0.93517 | 0.62121 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76780 | 76780 | SRR25374426 | SRX21113472 | SRS18382066 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 B05 | GSM7655722 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 B05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655722 | GSM7655722: ExVi2Red 01 B05; Danio rerio; RNA Seq | GSM7655722 r1 | GSM7655722 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21247_Track-51564_R1.fastq.gz | fastq | 39210908.0 | 515933.0 | GSM7655722 r1 | 0:76 | A:10287821;C:9187861;G:9206063;T:10528196;N:967 | 76 | 10287821 | 9187861 | 9206063 | 10528196 | 967 | SRX21113472 | SRS18382066 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.86501 | 0.0627 | 0.91007 | 0.61738 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76781 | 76781 | SRR25374427 | SRX21113471 | SRS18382065 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 C05 | GSM7655721 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 C05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655721 | GSM7655721: ExVi2Red 01 C05; Danio rerio; RNA Seq | GSM7655721 r1 | GSM7655721 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21248_Track-51565_R1.fastq.gz | fastq | 38625252.0 | 508227.0 | GSM7655721 r1 | 0:76 | A:10080873;C:9030644;G:8994423;T:10518327;N:985 | 76 | 10080873 | 9030644 | 8994423 | 10518327 | 985 | SRX21113471 | SRS18382065 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.86695 | 0.06747 | 0.93837 | 0.67272 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76782 | 76782 | SRR25374428 | SRX21113470 | SRS18382063 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 D05 | GSM7655720 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 D05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655720 | GSM7655720: ExVi2Red 01 D05; Danio rerio; RNA Seq | GSM7655720 r1 | GSM7655720 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21249_Track-51566_R1.fastq.gz | fastq | 38599488.0 | 507888.0 | GSM7655720 r1 | 0:76 | A:10171275;C:8965675;G:8953753;T:10507855;N:930 | 76 | 10171275 | 8965675 | 8953753 | 10507855 | 930 | SRX21113470 | SRS18382063 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.84344 | 0.069 | 0.93519 | 0.66364 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76783 | 76783 | SRR25374429 | SRX21113469 | SRS18382064 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | UHR 01 E05 | GSM7655719 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | UHR 01 E05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655719 | GSM7655719: UHR 01 E05; Danio rerio; RNA Seq | GSM7655719 r1 | GSM7655719 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21250_Track-51567_R1.fastq.gz | fastq | 37809468.0 | 497493.0 | GSM7655719 r1 | 0:76 | A:9802568;C:8894462;G:9020819;T:10090613;N:1006 | 76 | 9802568 | 8894462 | 9020819 | 10090613 | 1006 | SRX21113469 | SRS18382064 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.00309 | 0.00234 | 0.99894 | 0.71653 | 76 | T | under 1.2% mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76784 | 76784 | SRR25374430 | SRX21113468 | SRS18382062 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 F05 | GSM7655718 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 F05 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655718 | GSM7655718: ExVi2Red 01 F05; Danio rerio; RNA Seq | GSM7655718 r1 | GSM7655718 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21251_Track-51568_R1.fastq.gz | fastq | 27209672.0 | 358022.0 | GSM7655718 r1 | 0:76 | A:7189506;C:6365576;G:6376421;T:7277585;N:584 | 76 | 7189506 | 6365576 | 6376421 | 7277585 | 584 | SRX21113468 | SRS18382062 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.89002 | 0.05915 | 0.8869 | 0.58584 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||||||
| 76785 | 76785 | SRR25374431 | SRX21113467 | SRS18382061 | SRP450614 | PRJNA996961 | Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling. | GSE237867 | Transcriptome Analysis | Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single molecule RNA detection we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells. We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was … | pubmed:38924394 | ExVi2Red 01 H08 | GSM7655693 | source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing | ExVi2Red 01 H08 | Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences. Trimmed reads were aligned to the zebrafish genome GRCz10 using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis cells with more than 800 detected genes were utilized. Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters. Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes FishEnrichR was utilized. As background genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv | pancreas | The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia. Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium magnesium ThermoFisher 14040141 along with the appropriate concentration of D Glucose. The islets were allowed to equilibrate for 5 min. Subsequently the entire 24 well plate was photoconverted using a 405 nm LED array Loctite 1167593 for 3 seconds. The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch. An internal timer using an LED controller Loctite 1359255 was utilized for precise timing of light exposure. | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | 4 mpf Tgins:CaMPARI zebrafish | tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion | GSM7655693 | GSM7655693: ExVi2Red 01 H08; Danio rerio; RNA Seq | GSM7655693 r1 | GSM7655693 | 1 | The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4°C. The supernatant was carefully discarded and the pellet re suspended in 500 µl of HBSS without xxx+ Mg2+. To remove debris the solution was passed over a 30 µm cell filter Miltenyi Biotec 130 041 407. To remove dead cells calcein violet ThermoFisher C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes. The single cell preparation was sorted through 100 µm nozzle. The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara. For this islets were isolated photoconverted ex vivo dissociated and FAC sorted as described above. β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM. Photoconversion was defined as a high red to green ratio. For FACS of each condition index sorting was utilized and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB. For each condition a total of 93 cells were collected for profiling. Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al. Scientific Reports 2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP450614 | loader:fastq load.py | L21277_Track-51593_R1.fastq.gz | fastq | 35576816.0 | 468116.0 | GSM7655693 r1 | 0:76 | A:9738994;C:7920726;G:7964832;T:9951202;N:1062 | 76 | 9738994 | 7920726 | 7964832 | 9951202 | 1062 | SRX21113467 | SRS18382061 | SRA1676813 | Regeneration and Stress Biology, IRIBHM, ULB | Regeneration and Stress Biology, IRIBHM, ULB | 1 | 0.82033 | 0.12428 | 0.92837 | 0.61179 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Belgium | 2023-07-20 | Adult | Adult | Pancreas | Endocrine System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;