run_metadata
73 rows where experiment.library_strategy = "RNA-Seq", technology = "10x" 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 | |||||||||||||||||||||||
| 43994 | 43994 | SRR6811821 | SRX3768861 | SRS3023378 | SRP121343 | PRJNA415636 | Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars | GSE106121 | Other | A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes. | pubmed:29644996 | Pancreas 3 endo mRNA | GSM3032164 | source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult | Pancreas 3 endo mRNA | Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. | Primary pancreatic islet | Single cell dissociation. 10X Genomics Chromium | strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult | GSM3032164 | GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq | GSM3032164 | 1 | Single cell dissociation. 10X Genomics Chromium | GEO Accession:GSM3032164 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP121343 | P7endo_wt_R1.fastq.gz P7endo_wt_R2.fastq.gz | fastq fastq | 41593781900.0 | 335433725.0 | GSM3032164 r1 | 0:26 1:98 | A:11833690021;C:9547054378;G:9724089290;T:10470148302;N:18799909 | 26 | 98 | 11833690021 | 9547054378 | 9724089290 | 10470148302 | 18799909 | SRX3768861 | SRS3023378 | SRA623333 | GEO | Max Delbrück Center | 2 | 0.00308 | 0.92936 | 0.00192 | 0.05695 | 0.9973 | 0.8686 | 0.45945 | 0.58814 | 26 | 98 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2018-03-06 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||
| 50847 | 50847 | SRR8312900 | SRX5126276 | SRS4139398 | SRP173304 | PRJNA509469 | Single cell RNA sequencing of zebrafish pancreatic cells | GSE123662 | Other | The pancreatic beta cells regulate blood glucose levels by secreting the hormone insulin in response to increasing glucose levels. Recent work has identified molecular and functional heterogeneity among the beta cell community. To ontain an unbiased picture into the molecular heterogeneity present in zebrafish pancreatic cells we performed droplet based next generation sequencing of individual pancreatic cells. Using unsupervised clustering we could identify all the major cell types present in the pancreas. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile pancreatic cells from zebrafish. Pancreatic islets from six animals were dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense'. Genome sequence and filtered annotation were then used as input to the 'mkref' command of Cell Ranger to build the appropriate Cellranger Reference. | pubmed:32694805 | 2mpf Pancreas | GSM3509161 | tissue:pancreatic cells|age:2mpf|strain:Tgins:BB1.0L|disease state:Normal | 2mpf Pancreas | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ‘ expect cells’ set to 5000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger options: ‘ attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: csv format with rows as genes and columns as cells | pancreatic cells | Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol. | age:2mpf|strain:Tgins:BB1.0L|disease state:Normal | GSM3509161 | GSM3509161: 2mpf Pancreas; Danio rerio; RNA Seq | GSM3509161 | 1 | Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 5000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer's protocol. | GEO Accession:GSM3509161 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP173304 | s2mpf_R1.fastq.gz s2mpf_R2.fastq.gz | fastq fastq | 3682641276.0 | 44369172.0 | GSM3509161 r1 | 0:26 1:57 | A:950388419;C:876060179;G:944476013;T:911635661;N:81004 | 26 | 57 | 950388419 | 876060179 | 944476013 | 911635661 | 81004 | SRX5126276 | SRS4139398 | SRA822849 | GEO | Single Cell Endocrinology, IRIBHM | 2 | 0.00373 | 0.9564 | 0.0008 | 0.03195 | 0.99508 | 0.9024 | 0.38273 | 0.59374 | 26 | 57 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Belgium | 2018-12-11 | Juvenile | Juvenile | Pancreas | Endocrine System | ||||||||||||
| 50860 | 50860 | SRR8315379 | SRX5128211 | SRS4141333 | SRP173374 | PRJNA509801 | Single cell sequencing analysis of the zebrafish pineal gland | GSE123778 | Transcriptome Analysis | The purpose of this study was to genetically describe the different pineal cell types and in particular the type of cells expressing the gene agrp2. The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample twenty adult pineal glands were dissected and processed together. | pubmed:31178320 | scSeq2 | GSM3511193 | source name:pineal glands|tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month | scSeq2 | Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10 Ensembl release 91 annotations and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally reads were aligned UMIs processed and transcripts counted to generate gene/barcode matrices which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files. | pineal glands | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month | GSM3511193 | GSM3511193: scSeq2; Danio rerio; RNA Seq | GSM3511193 | 1 | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | GEO Accession:GSM3511193 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP173374 | scSeq2_L001_R1_001.fastq.gz scSeq2_L001_R2_001.fastq.gz | fastq fastq | 29063395032.0 | 234382218.0 | GSM3511193 r1 | 0:26 1:98 | A:8483803116;C:5981698341;G:6389916823;T:8203926541;N:4050211 | 26 | 98 | 8483803116 | 5981698341 | 6389916823 | 8203926541 | 4050211 | SRX5128211 | SRS4141333 | SRA823034 | GEO | Tel Aviv University | 2 | 0.00394 | 0.91121 | 0.00091 | 0.19356 | 0.99389 | 0.80984 | 0.23443 | 0.48501 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Israel | 2018-12-13 | Adult | Adult | Pineal Gland | Endocrine System | ||||||||||||
| 50861 | 50861 | SRR8315380 | SRX5128211 | SRS4141333 | SRP173374 | PRJNA509801 | Single cell sequencing analysis of the zebrafish pineal gland | GSE123778 | Transcriptome Analysis | The purpose of this study was to genetically describe the different pineal cell types and in particular the type of cells expressing the gene agrp2. The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample twenty adult pineal glands were dissected and processed together. | pubmed:31178320 | scSeq2 | GSM3511193 | source name:pineal glands|tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month | scSeq2 | Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10 Ensembl release 91 annotations and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally reads were aligned UMIs processed and transcripts counted to generate gene/barcode matrices which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files. | pineal glands | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month | GSM3511193 | GSM3511193: scSeq2; Danio rerio; RNA Seq | GSM3511193 | 1 | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | GEO Accession:GSM3511193 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP173374 | scSeq2_L002_R1_001.fastq.gz scSeq2_L002_R2_001.fastq.gz | fastq fastq | 29003313560.0 | 233897690.0 | GSM3511193 r2 | 0:26 1:98 | A:8453400725;C:5974567982;G:6382782124;T:8189587364;N:2975365 | 26 | 98 | 8453400725 | 5974567982 | 6382782124 | 8189587364 | 2975365 | SRX5128211 | SRS4141333 | SRA823034 | GEO | Tel Aviv University | 2 | 0.00378 | 0.91135 | 0.00087 | 0.19518 | 0.99413 | 0.80937 | 0.20454 | 0.48353 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Israel | 2018-12-13 | Adult | Adult | Pineal Gland | Endocrine System | ||||||||||||
| 50862 | 50862 | SRR8315377 | SRX5128210 | SRS4141331 | SRP173374 | PRJNA509801 | Single cell sequencing analysis of the zebrafish pineal gland | GSE123778 | Transcriptome Analysis | The purpose of this study was to genetically describe the different pineal cell types and in particular the type of cells expressing the gene agrp2. The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample twenty adult pineal glands were dissected and processed together. | pubmed:31178320 | scSeq1 | GSM3511192 | source name:pineal glands|tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month | scSeq1 | Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10 Ensembl release 91 annotations and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally reads were aligned UMIs processed and transcripts counted to generate gene/barcode matrices which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files. | pineal glands | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month | GSM3511192 | GSM3511192: scSeq1; Danio rerio; RNA Seq | GSM3511192 | 1 | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | GEO Accession:GSM3511192 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP173374 | scSeq1_L001_R1_001.fastq.gz scSeq1_L001_R2_001.fastq.gz | fastq fastq | 15101906060.0 | 121789565.0 | GSM3511192 r1 | 0:26 1:98 | A:4389085504;C:3222094251;G:3483928123;T:3991523000;N:15275182 | 26 | 98 | 4389085504 | 3222094251 | 3483928123 | 3991523000 | 15275182 | SRX5128210 | SRS4141331 | SRA823034 | GEO | Tel Aviv University | 2 | 0.00534 | 0.86489 | 0.00171 | 0.14238 | 0.99204 | 0.85263 | 0.2798 | 0.50024 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Israel | 2018-12-13 | Adult | Adult | Pineal Gland | Endocrine System | ||||||||||||
| 50863 | 50863 | SRR8315378 | SRX5128210 | SRS4141331 | SRP173374 | PRJNA509801 | Single cell sequencing analysis of the zebrafish pineal gland | GSE123778 | Transcriptome Analysis | The purpose of this study was to genetically describe the different pineal cell types and in particular the type of cells expressing the gene agrp2. The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample twenty adult pineal glands were dissected and processed together. | pubmed:31178320 | scSeq1 | GSM3511192 | source name:pineal glands|tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month | scSeq1 | Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10 Ensembl release 91 annotations and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally reads were aligned UMIs processed and transcripts counted to generate gene/barcode matrices which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files. | pineal glands | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | tissue:pineal glands|transgenic background:TgBACagrp2:Gal4 VP16tlv05; TgUAS:nfsb mCherryc264; Tgfoxd3:EGFPzf104|age:6 month 12 month | GSM3511192 | GSM3511192: scSeq1; Danio rerio; RNA Seq | GSM3511192 | 1 | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | GEO Accession:GSM3511192 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP173374 | scSeq1_L002_R1_001.fastq.gz scSeq1_L002_R2_001.fastq.gz | fastq fastq | 12784244380.0 | 103098745.0 | GSM3511192 r2 | 0:26 1:98 | A:3711546705;C:2726963744;G:2944583108;T:3391689087;N:9461736 | 26 | 98 | 3711546705 | 2726963744 | 2944583108 | 3391689087 | 9461736 | SRX5128210 | SRS4141331 | SRA823034 | GEO | Tel Aviv University | 2 | 0.00543 | 0.85703 | 0.00187 | 0.14217 | 0.99222 | 0.85665 | 0.27512 | 0.51728 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Israel | 2018-12-13 | Adult | Adult | Pineal Gland | Endocrine System | ||||||||||||
| 52953 | 52953 | SRR9609654 | SRX6373048 | SRS5034105 | SRP212225 | PRJNA551501 | Single cell RNA sequencing of zebrafish thyroid cells | GSE133466 | Transcriptome Analysis | The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes surrounded by thyroid follicular epithelial cells or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes we performed droplet based next generation sequencing of individual thyrod gland cells. Using unsupervised clustering we could identify all the major cell types present in the thyroid gland. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile thyroid cells from zebrafish. Thyroid gland was enzymatically dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' … | 8mpf Thyroid | GSM3909772 | tissue:thyroid gland|treatment:8mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal | 8mpf Thyroid | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ‘ expect cells’ set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger options: ‘ attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells. | thyroid gland | Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol. | treatment:8mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal | GSM3909772 | GSM3909772: 8mpf Thyroid; Danio rerio; RNA Seq | GSM3909772 | 1 | Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP212225 | L38696_Track-76232_R1.fastq.gz L38696_Track-76232_R2.fastq.gz | fastq fastq | 9752526168.0 | 116101502.0 | GSM3909772 r1 | 0:28 1:56 | A:2760523285;C:2129359977;G:2225570954;T:2632796182;N:4275770 | 28 | 56 | 2760523285 | 2129359977 | 2225570954 | 2632796182 | 4275770 | SRX6373048 | SRS5034105 | SRA914541 | GEO | Singh Lab, IRIBHM | 2 | 0.00831 | 0.90972 | 0.00332 | 0.2088 | 0.99157 | 0.80182 | 0.40796 | 0.56239 | 28 | 56 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Belgium | 2019-06-27 | Adult | Adult | Thyroid | Endocrine System | ||||||||||||||
| 52954 | 52954 | SRR9609653 | SRX6373047 | SRS5034104 | SRP212225 | PRJNA551501 | Single cell RNA sequencing of zebrafish thyroid cells | GSE133466 | Transcriptome Analysis | The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes surrounded by thyroid follicular epithelial cells or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes we performed droplet based next generation sequencing of individual thyrod gland cells. Using unsupervised clustering we could identify all the major cell types present in the thyroid gland. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile thyroid cells from zebrafish. Thyroid gland was enzymatically dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' … | 2mpf Thyroid | GSM3909771 | tissue:thyroid gland|treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal | 2mpf Thyroid | The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ‘ expect cells’ set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger options: ‘ attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells. | thyroid gland | Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol. | treatment:2mpf|strain:Tgtg:mVenus T2A NTR|tag:Normal | GSM3909771 | GSM3909771: 2mpf Thyroid; Danio rerio; RNA Seq | GSM3909771 | 1 | Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer's protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP212225 | L38695_Track-76231_R2.fastq.gz L38695_Track-76231_R1.fastq.gz | fastq fastq | 9092057268.0 | 108238777.0 | GSM3909771 r1 | 0:28 1:56 | A:2584354341;C:1956113829;G:2086486284;T:2461142498;N:3960316 | 28 | 56 | 2584354341 | 1956113829 | 2086486284 | 2461142498 | 3960316 | SRX6373047 | SRS5034104 | SRA914541 | GEO | Singh Lab, IRIBHM | 2 | 0.01005 | 0.87575 | 0.00435 | 0.23392 | 0.99192 | 0.80344 | 0.39812 | 0.53402 | 28 | 56 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Belgium | 2019-06-27 | Juvenile | Juvenile | Thyroid | Endocrine System | ||||||||||||||
| 58918 | 58918 | SRR11540947 | SRX8111243 | SRS6476317 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Transplant | GSM4474605 | source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | Transplant | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | GSM4474605 | GSM4474605: Transplant; Danio rerio; RNA Seq | GSM4474605 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474605 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | ubieGFP_Pit-Endo-transp_3mpf-m-1_S25_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-1_S25_L001_R1_001.fastq.gz | fastq fastq | 32025333121.0 | 217126081.0 | GSM4474605 r1 | 0:27 1:120.50 | A:9314654962;C:6522735572;G:6826173512;T:9343095148;N:18673927 | 27 | 120 | 9314654962 | 6522735572 | 6826173512 | 9343095148 | 18673927 | SRX8111243 | SRS6476317 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00161 | 0.90845 | 0.00057 | 0.11751 | 0.99687 | 0.82771 | 0.47738 | 0.59877 | 27 | 121 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58919 | 58919 | SRR11540948 | SRX8111243 | SRS6476317 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Transplant | GSM4474605 | source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | Transplant | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | GSM4474605 | GSM4474605: Transplant; Danio rerio; RNA Seq | GSM4474605 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474605 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | ubieGFP_Pit-Endo-transp_3mpf-m-2_S26_L001_R1_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-2_S26_L001_R2_001.fastq.gz | fastq fastq | 37830323844.0 | 256490571.0 | GSM4474605 r2 | 0:27 1:120.49 | A:11021068490;C:7699701868;G:8072819621;T:11014855601;N:21878264 | 27 | 120 | 11021068490 | 7699701868 | 8072819621 | 11014855601 | 21878264 | SRX8111243 | SRS6476317 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00167 | 0.90711 | 0.00066 | 0.11917 | 0.99663 | 0.83 | 0.53886 | 0.59796 | 27 | 120 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58920 | 58920 | SRR11540949 | SRX8111243 | SRS6476317 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Transplant | GSM4474605 | source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | Transplant | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | GSM4474605 | GSM4474605: Transplant; Danio rerio; RNA Seq | GSM4474605 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474605 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | ubieGFP_Pit-Endo-transp_3mpf-m-3_S27_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-3_S27_L001_R1_001.fastq.gz | fastq fastq | 28249532732.0 | 191530324.0 | GSM4474605 r3 | 0:27 1:120.49 | A:8193419181;C:5751619572;G:6039589822;T:8248615264;N:16288893 | 27 | 120 | 8193419181 | 5751619572 | 6039589822 | 8248615264 | 16288893 | SRX8111243 | SRS6476317 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.0017 | 0.90552 | 0.0006 | 0.11697 | 0.99667 | 0.82576 | 0.54976 | 0.60065 | 27 | 120 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58921 | 58921 | SRR11540950 | SRX8111243 | SRS6476317 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Transplant | GSM4474605 | source name:Pituitary|genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | Transplant | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:mosaic animal: ubi:loxP EGFP loxP mCherry + bact:loxP TagBFP loxP dsRed|treatment:graft transplantation during early embryogenesis|tissue:Pituitary|age:3 month | GSM4474605 | GSM4474605: Transplant; Danio rerio; RNA Seq | GSM4474605 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474605 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | ubieGFP_Pit-Endo-transp_3mpf-m-4_S28_L001_R2_001.fastq.gz ubieGFP_Pit-Endo-transp_3mpf-m-4_S28_L001_R1_001.fastq.gz | fastq fastq | 28226688209.0 | 191373742.0 | GSM4474605 r4 | 0:27 1:120.50 | A:8176659734;C:5765390596;G:6034905304;T:8233376515;N:16356060 | 27 | 120 | 8176659734 | 5765390596 | 6034905304 | 8233376515 | 16356060 | SRX8111243 | SRS6476317 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00163 | 0.90646 | 0.00056 | 0.11667 | 0.99667 | 0.82603 | 0.57 | 0.59607 | 27 | 121 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58922 | 58922 | SRR11540943 | SRX8111242 | SRS6476316 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Male1 | GSM4474604 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Male1 | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474604 | GSM4474604: Male1; Danio rerio; RNA Seq | GSM4474604 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474604 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M1_Pituitary_Sox17creERUbiGtR-1_S13_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-1_S13_L001_R1_001.fastq.gz | fastq fastq | 31605717037.0 | 214359798.0 | GSM4474604 r1 | 0:27 1:120.44 | A:9104842871;C:6521304311;G:6857625119;T:9101526427;N:20418309 | 27 | 120 | 9104842871 | 6521304311 | 6857625119 | 9101526427 | 20418309 | SRX8111242 | SRS6476316 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00259 | 0.88483 | 0.00097 | 0.20321 | 0.995 | 0.80079 | 0.52597 | 0.56862 | 27 | 120 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58923 | 58923 | SRR11540944 | SRX8111242 | SRS6476316 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Male1 | GSM4474604 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Male1 | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474604 | GSM4474604: Male1; Danio rerio; RNA Seq | GSM4474604 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474604 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M1_Pituitary_Sox17creERUbiGtR-2_S14_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-2_S14_L001_R1_001.fastq.gz | fastq fastq | 27674233334.0 | 187694200.0 | GSM4474604 r2 | 0:27 1:120.44 | A:7958817473;C:5737419593;G:6003046001;T:7957045184;N:17905083 | 27 | 120 | 7958817473 | 5737419593 | 6003046001 | 7957045184 | 17905083 | SRX8111242 | SRS6476316 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00275 | 0.88312 | 0.00108 | 0.20427 | 0.99478 | 0.80608 | 0.47634 | 0.56166 | 27 | 120 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58924 | 58924 | SRR11540945 | SRX8111242 | SRS6476316 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Male1 | GSM4474604 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Male1 | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474604 | GSM4474604: Male1; Danio rerio; RNA Seq | GSM4474604 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474604 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M1_Pituitary_Sox17creERUbiGtR-3_S15_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-3_S15_L001_R1_001.fastq.gz | fastq fastq | 35522886586.0 | 240929767.0 | GSM4474604 r3 | 0:27 1:120.44 | A:10224992422;C:7358725736;G:7719740991;T:10196515119;N:22912318 | 27 | 120 | 10224992422 | 7358725736 | 7719740991 | 10196515119 | 22912318 | SRX8111242 | SRS6476316 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.0028 | 0.88842 | 0.00103 | 0.20371 | 0.99468 | 0.80127 | 0.46449 | 0.4682 | 27 | 121 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58925 | 58925 | SRR11540946 | SRX8111242 | SRS6476316 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Male1 | GSM4474604 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Male1 | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474604 | GSM4474604: Male1; Danio rerio; RNA Seq | GSM4474604 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474604 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M1_Pituitary_Sox17creERUbiGtR-4_S16_L001_R2_001.fastq.gz M1_Pituitary_Sox17creERUbiGtR-4_S16_L001_R1_001.fastq.gz | fastq fastq | 22322824317.0 | 151402860.0 | GSM4474604 r4 | 0:27 1:120.44 | A:6438472506;C:4603208282;G:4838569546;T:6428191408;N:14382575 | 27 | 120 | 6438472506 | 4603208282 | 4838569546 | 6428191408 | 14382575 | SRX8111242 | SRS6476316 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00247 | 0.88259 | 0.00091 | 0.20556 | 0.99521 | 0.80395 | 0.47651 | 0.55966 | 27 | 121 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58926 | 58926 | SRR11540939 | SRX8111241 | SRS6476315 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Males | GSM4474603 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Males | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474603 | GSM4474603: Males; Danio rerio; RNA Seq | GSM4474603 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474603 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M_Pituitary_Sox17creERUbiGtR-1_S9_L001_R1_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-1_S9_L001_R2_001.fastq.gz | fastq fastq | 47824931084.0 | 324315726.0 | GSM4474603 r1 | 0:27 1:120.46 | A:13805207199;C:9886339394;G:10399128349;T:13703273256;N:30982886 | 27 | 120 | 13805207199 | 9886339394 | 10399128349 | 13703273256 | 30982886 | SRX8111241 | SRS6476315 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00277 | 0.89029 | 0.00096 | 0.16996 | 0.99462 | 0.81481 | 0.49279 | 0.59136 | 27 | 121 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58927 | 58927 | SRR11540940 | SRX8111241 | SRS6476315 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Males | GSM4474603 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Males | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474603 | GSM4474603: Males; Danio rerio; RNA Seq | GSM4474603 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474603 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M_Pituitary_Sox17creERUbiGtR-2_S10_L001_R2_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-2_S10_L001_R1_001.fastq.gz | fastq fastq | 32243370700.0 | 218650680.0 | GSM4474603 r2 | 0:27 1:120.47 | A:9305381092;C:6663053359;G:7018746988;T:9235440820;N:20748441 | 27 | 120 | 9305381092 | 6663053359 | 7018746988 | 9235440820 | 20748441 | SRX8111241 | SRS6476315 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00277 | 0.8884 | 0.00091 | 0.1672 | 0.99458 | 0.81533 | 0.51123 | 0.58754 | 27 | 120 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58928 | 58928 | SRR11540941 | SRX8111241 | SRS6476315 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Males | GSM4474603 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Males | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474603 | GSM4474603: Males; Danio rerio; RNA Seq | GSM4474603 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474603 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M_Pituitary_Sox17creERUbiGtR-3_S11_L001_R1_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-3_S11_L001_R2_001.fastq.gz | fastq fastq | 28915149568.0 | 196083542.0 | GSM4474603 r3 | 0:27 1:120.46 | A:8347281799;C:5984386507;G:6301924708;T:8262927533;N:18629021 | 27 | 120 | 8347281799 | 5984386507 | 6301924708 | 8262927533 | 18629021 | SRX8111241 | SRS6476315 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00281 | 0.88705 | 0.00088 | 0.16827 | 0.99454 | 0.81233 | 0.49184 | 0.58837 | 27 | 118 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 58929 | 58929 | SRR11540942 | SRX8111241 | SRS6476315 | SRP256300 | PRJNA625098 | Single cell transcriptomic analysis of endoderm derived cell lineages contribution in pituitary | GSE148591 | Transcriptome Analysis | Single cell transcriptomic analysis of pituitary gland from adult zebrafish that had specifically cells labeled with endoderm lineage by different strategies. The goal of this study is to examine the contribution of endoderm derived cell in the pituitary of vertebrate animals. Overall design: We applied two strategies for labeling the endoderm derived cell in the pituitaries of zebrafish. The contribution of endoderm derived cells and the cell heterogeneity was later analyzed and resolved through constructing the single cell transcriptome through 10X Genomic pipeline. The first strategy is through endodermal lineage tracing techniques by Sox17 driven Cre recombinase conjuncted with an estrogen receptor Sox17:CreERT2 which allows us to induce the conversion by addition of tamoxifen. We are able to identify the endoderm derived cell by microscopic observation with expression of mCherry gene from EGFP background. We made two single cell transcriptomic libraries by this strategy: the males library file names started with M Pituitary Sox17creERUbiGtR was derived by pooling 6 adult zebrafish pituitaries with moderate Sox17:CreERT2 conversion rate. The male1 library file names started with M1 Pituitary Sox17creERUbiGtR was derived from the pituitary from a male zebrafish with high conversion rate. The second strategy is through transplant of taram a mRNA injected GFP+ embryo to limit the cell into endoderm lineage. The treated embryonic cells were then injected into a BFP+ wild type embryo for tracing. The endoderm derived cells can be identify by expression of GFP. We made one single cell transcriptomic library by this strategy: the ubeGFP transplanted file names started with ubieGFP Pit Endo transp library was derived from pooling of pituitaries from adult transplanted fish. | pubmed:33093109 | Males | GSM4474603 | source name:Pituitary|genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | Males | 10X Genomic Cellranger v3.0.0 was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against in house built transcriptome index containing transgenic sequences EGFP mCherry and TagBFP. QC step for the library was performed along with the Cellranger alignment process. The raw count matrices were filtered for genes observed in at least 5 cells and cells that had at least 500 unique genes expressed. To reduce the batch effects caused by the different strategies we aligned the scaled data based on the CCA analysis by R package Seurat v2.4.0 to supress the variance introduced between libraries to generate an aggregated library. The aggregated library was further filtered less than 0.04 mitochondrial gene expression and with 200 to 2500 unique genes. With the aligned CCA space we found cluster by Louvain clustering with 0.1 resolution and performed low dimensional embedding by UMAP through functions in Seurat. The assignment of cluster identity was done by examine the marker genes for different cell types reported in literatures. Genome build: GRCz11 Supplementary files format and content: tab delimited file with cell barcode information tab delimited file with gene names sparse matrix file with raw count associated with previous two files | Pituitary | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | 6mpf animals Males and Male1 and 3mpf animal for transplant | genotype:Sox17:CreERT2;ubi:loxP EGFP loxP mCherry|treatment:4OH Tamoxifen|tissue:Pituitary|age:6 month | GSM4474603 | GSM4474603: Males; Danio rerio; RNA Seq | GSM4474603 | 1 | Single cell was partitioned through Chromium platform 10X Genomic which encapsulate each cell in individual GEMs. The cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs. The version 2 of Chromium Single Cell three prime Reagent Kits was used for this RNA extraction step. post cell barcoding the extracted RNA the GEMs were lysis for further fragmentation and ligation of illumina P5 and P7 ends with the version 2 of Chromium Single Cell three prime Reagent Kits. Two size selections were performed for long fragments > 1000 bps and short fragments < 1000 bps before fragmentation and post finalization respectively. | GEO Accession:GSM4474603 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP256300 | M_Pituitary_Sox17creERUbiGtR-4_S12_L001_R2_001.fastq.gz M_Pituitary_Sox17creERUbiGtR-4_S12_L001_R1_001.fastq.gz | fastq fastq | 33158543550.0 | 224853573.0 | GSM4474603 r4 | 0:27 1:120.47 | A:9576940269;C:6855014912;G:7203590871;T:9501520990;N:21476508 | 27 | 120 | 9576940269 | 6855014912 | 7203590871 | 9501520990 | 21476508 | SRX8111241 | SRS6476315 | SRA1065111 | GEO | Crump Lab, Stem Cell, USC | 2 | 0.00273 | 0.8878 | 0.00089 | 0.16918 | 0.99494 | 0.81801 | 0.51694 | 0.58973 | 27 | 121 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United States | 2020-04-13 | Adult | Adult | Pituitary Gland | Endocrine System | |||||||||||
| 63128 | 63128 | SRR13616487 | SRX10009741 | SRS8178664 | SRP304424 | PRJNA699078 | Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration | GSE166052 | Transcriptome Analysis | To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics. | pubmed:35088828 | Pancreas 14dpa | GSM5060849 | tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 14 days post MTZ | Pancreas 14dpa | bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices | Zebrafish pancreas | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 14 days post MTZ | GSM5060849 | GSM5060849: Pancreas 14dpa; Danio rerio; RNA Seq | GSM5060849 | 1 | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | GEO Accession:GSM5060849 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP304424 | L59491_Track-100378_R1.fastq.gz L59491_Track-100378_R2.fastq.gz | fastq fastq | 21882647280.0 | 168328056.0 | GSM5060849 r1 | 0:29 1:101 | A:5304415368;C:5193690448;G:5721535951;T:5662241808;N:763705 | 29 | 101 | 5304415368 | 5193690448 | 5721535951 | 5662241808 | 763705 | SRX10009741 | SRS8178664 | SRA1190924 | GEO | Ninov Lab, CRTD, TU Dresden | 2 | 0.0137 | 0.94318 | 0.00185 | 0.03707 | 0.99263 | 0.91078 | 0.60061 | 0.58256 | 29 | 101 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-02-02 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||
| 63129 | 63129 | SRR13616486 | SRX10009740 | SRS8178663 | SRP304424 | PRJNA699078 | Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration | GSE166052 | Transcriptome Analysis | To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics. | pubmed:35088828 | Pancreas 7dpa | GSM5060848 | tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 7 days post MTZ | Pancreas 7dpa | bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices | Zebrafish pancreas | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 7 days post MTZ | GSM5060848 | GSM5060848: Pancreas 7dpa; Danio rerio; RNA Seq | GSM5060848 | 1 | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | GEO Accession:GSM5060848 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP304424 | L47897_Track-91889_R1.fastq.gz L47897_Track-91889_R2.fastq.gz | fastq fastq | 11982402020.0 | 98216410.0 | GSM5060848 r1 | 0:29 1:93 | A:3162707284;C:2774571882;G:2736678637;T:3307378654;N:1065563 | 29 | 93 | 3162707284 | 2774571882 | 2736678637 | 3307378654 | 1065563 | SRX10009740 | SRS8178663 | SRA1190924 | GEO | Ninov Lab, CRTD, TU Dresden | 2 | 0.01025 | 0.93044 | 0.00221 | 0.066 | 0.98938 | 0.85823 | 0.52941 | 0.62147 | 29 | 93 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-02-02 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||
| 63130 | 63130 | SRR13616485 | SRX10009739 | SRS8178662 | SRP304424 | PRJNA699078 | Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration | GSE166052 | Transcriptome Analysis | To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics. | pubmed:35088828 | Pancreas 2dpa | GSM5060847 | tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 2 days post MTZ | Pancreas 2dpa | bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices | Zebrafish pancreas | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 2 days post MTZ | GSM5060847 | GSM5060847: Pancreas 2dpa; Danio rerio; RNA Seq | GSM5060847 | 1 | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | GEO Accession:GSM5060847 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP304424 | L47899_Track-88823_R1.fastq.gz L47899_Track-88823_R2.fastq.gz | fastq fastq | 12079250378.0 | 99010249.0 | GSM5060847 r1 | 0:29 1:93 | A:3187642396;C:2755358695;G:2795295173;T:3340653508;N:300606 | 29 | 93 | 3187642396 | 2755358695 | 2795295173 | 3340653508 | 300606 | SRX10009739 | SRS8178662 | SRA1190924 | GEO | Ninov Lab, CRTD, TU Dresden | 2 | 0.00631 | 0.94202 | 0.00135 | 0.0615 | 0.99123 | 0.84307 | 0.55742 | 0.56593 | 29 | 93 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-02-02 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||
| 63131 | 63131 | SRR13616484 | SRX10009738 | SRS8178661 | SRP304424 | PRJNA699078 | Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration | GSE166052 | Transcriptome Analysis | To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics. | pubmed:35088828 | Pancreas 0dpa | GSM5060846 | tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 0 days post MTZ | Pancreas 0dpa | bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices | Zebrafish pancreas | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 0 days post MTZ | GSM5060846 | GSM5060846: Pancreas 0dpa; Danio rerio; RNA Seq | GSM5060846 | 1 | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | GEO Accession:GSM5060846 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP304424 | L59306_Track-100369_R1.fastq.gz L59306_Track-100369_R2.fastq.gz | fastq fastq | 19138165410.0 | 147216657.0 | GSM5060846 r1 | 0:29 1:101 | A:4905247743;C:4584481588;G:4969548524;T:4678220753;N:666802 | 29 | 101 | 4905247743 | 4584481588 | 4969548524 | 4678220753 | 666802 | SRX10009738 | SRS8178661 | SRA1190924 | GEO | Ninov Lab, CRTD, TU Dresden | 2 | 0.02866 | 0.88637 | 0.00798 | 0.14499 | 0.99105 | 0.87251 | 0.51922 | 0.57508 | 29 | 101 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-02-02 | Adult | Adult | Pancreas | Endocrine System | ||||||||||||
| 63132 | 63132 | SRR13616483 | SRX10009737 | SRS8178660 | SRP304424 | PRJNA699078 | Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration | GSE166052 | Transcriptome Analysis | To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics. | pubmed:35088828 | Pancreas Control | GSM5060845 | tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:Untreated|time point:Untreated | Pancreas Control | bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices | Zebrafish pancreas | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:Untreated|time point:Untreated | GSM5060845 | GSM5060845: Pancreas Control; Danio rerio; RNA Seq | GSM5060845 | 1 | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | GEO Accession:GSM5060845 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP304424 | L47898_Track-88822_R1.fastq.gz L47898_Track-88822_R2.fastq.gz | fastq fastq | 8952747472.0 | 73383176.0 | GSM5060845 r1 | 0:29 1:93 | A:2223721886;C:2087634305;G:2235052745;T:2406116444;N:222092 | 29 | 93 | 2223721886 | 2087634305 | 2235052745 | 2406116444 | 222092 | SRX10009737 | SRS8178660 | SRA1190924 | GEO | Ninov Lab, CRTD, TU Dresden | 2 | 0.00837 | 0.9475 | 0.00144 | 0.0366 | 0.99263 | 0.88759 | 0.58964 | 0.57851 | 29 | 93 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-02-02 | Adult | Adult | Pancreas | 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 |
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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");;