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
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,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,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,SRR31647631,SRX27010713,SRS23475006,SRP550229,PRJNA1195876,Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq],GSE283840,Transcriptome Analysis,Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however  the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here  we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably  amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms  which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover  Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically  Amh binds to its receptors  Bmpr2a/Bmpr1bb  which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however  the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype  amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.,,pubmed:40348785,,pituitary gland  WT,GSM8672963,,source name:pituitary gland|tissue:pituitary gland|genotype:WT|geo loc name:missing|collection date:missing,pituitary gland  WT,Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,pituitary gland,,post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer’s solution for 5 10 min  followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies  400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer  centrifuged 2000 rpm  5 min  4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.,,tissue:pituitary gland|genotype:WT,GSM8672963,GSM8672963: pituitary gland  WT; Danio rerio; RNA Seq,GSM8672963 r1,GSM8672963,1,post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer's solution for 5 10 min  followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies  400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer  centrifuged 2000 rpm  5 min  4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP550229,,,WT_R1.fq.gz WT_R2.fq.gz,fastq fastq,149500940700.0,498336469.0,GSM8672963 r1,0:150 1:150,A:49714239420;C:27445649314;G:26079818385;T:46259970208;N:1263373,150,150,,,49714239420,27445649314,26079818385,46259970208,1263373,SRX27010713,SRS23475006,SRA2029986,"Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences","Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-12-09,Undetermined,Undetermined,Pituitary Gland,Endocrine System
69988,SRR19217299,SRX15281308,SRS13012753,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9278,GSM6153483,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing,AB9278,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month,GSM6153483,GSM6153483: AB9278; Danio rerio; RNA Seq,GSM6153483 r1,GSM6153483,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz,fastq fastq,1259447780.0,11770540.0,GSM6153483 r1,0:92 1:15,A:305608913;C:313550706;G:363197186;T:277079546;N:11429,92,15,,,305608913,313550706,363197186,277079546,11429,SRX15281308,SRS13012753,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.94767,0.0,0.32091,0.0,0.89796,1.0,0.7545,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69989,SRR19217300,SRX15281307,SRS13012752,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9277,GSM6153482,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing,AB9277,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month,GSM6153482,GSM6153482: AB9277; Danio rerio; RNA Seq,GSM6153482 r1,GSM6153482,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz,fastq fastq,1130776107.0,10568001.0,GSM6153482 r1,0:92 1:15,A:288600700;C:269726443;G:310844405;T:261594352;N:10207,92,15,,,288600700,269726443,310844405,261594352,10207,SRX15281307,SRS13012752,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.94379,0.0,0.28638,0.0,0.86415,1.0,0.63321,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69990,SRR19217301,SRX15281306,SRS13012751,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9280,GSM6153481,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing,AB9280,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month,GSM6153481,GSM6153481: AB9280; Danio rerio; RNA Seq,GSM6153481 r1,GSM6153481,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz,fastq fastq,1172966528.0,10962304.0,GSM6153481 r1,0:92 1:15,A:311089180;C:274626206;G:310304031;T:276936052;N:11059,92,15,,,311089180,274626206,310304031,276936052,11059,SRX15281306,SRS13012751,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.92936,0.0,0.23628,0.0,0.86147,1.0,0.74656,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69991,SRR19217302,SRX15281305,SRS13012750,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9279,GSM6153480,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing,AB9279,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month,GSM6153480,GSM6153480: AB9279; Danio rerio; RNA Seq,GSM6153480 r1,GSM6153480,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz,fastq fastq,1383147163.0,12926609.0,GSM6153480 r1,0:92 1:15,A:364575971;C:320901229;G:367626618;T:330030659;N:12686,92,15,,,364575971,320901229,367626618,330030659,12686,SRX15281305,SRS13012750,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.92462,0.0,0.26743,0.0,0.8493,1.0,0.74133,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69992,SRR19217303,SRX15281304,SRS13012749,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB7418,GSM6153479,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing,AB7418,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf,GSM6153479,GSM6153479: AB7418; Danio rerio; RNA Seq,GSM6153479 r1,GSM6153479,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,,AB7418_SB350_S35_R1_001.fastq.gz AB7418_SB350_S35_R2_001.fastq.gz,fastq fastq,2468773944.0,29390166.0,GSM6153479 r1,0:69 1:15,A:764359919;C:520031317;G:592699381;T:591594655;N:88672,69,15,,,764359919,520031317,592699381,591594655,88672,SRX15281304,SRS13012749,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.85786,0.0,0.15143,0.0,0.84885,1.0,0.67021,,69,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Juvenile,Juvenile,Pituitary Gland,Endocrine System
69993,SRR19217304,SRX15281303,SRS13012748,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB7417,GSM6153478,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing,AB7417,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf,GSM6153478,GSM6153478: AB7417; Danio rerio; RNA Seq,GSM6153478 r1,GSM6153478,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,,AB7417_SB350_S24_R1_001.fastq.gz AB7417_SB350_S24_R2_001.fastq.gz,fastq fastq,2586526488.0,30791982.0,GSM6153478 r1,0:69 1:15,A:833353097;C:525447349;G:601496569;T:626135990;N:93483,69,15,,,833353097,525447349,601496569,626135990,93483,SRX15281303,SRS13012748,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.84125,0.0,0.10717,0.0,0.84768,1.0,0.63154,,69,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Juvenile,Juvenile,Pituitary Gland,Endocrine System