{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\" and tissue_curation = \"Pituitary Gland\"", "rows": [[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\u2013/\u2013 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\u2013/\u2013 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", null, "pubmed:39499852", null, "gnrh3 knockout  scRNAseq", "GSM8412848", null, "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\u00d7Genomics 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", null, "Five pituitaries were dissected from each gnrh3\u2013/\u2013 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 \u00d7 rpm for 5 minutes at 4\u00b0C  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 \u00b5m membrane filter at 28.5\u00b0C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 \u00b5L 6\u00d7Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C. 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 \u00b5m pore cell strainer. post centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  the supernatant was removed  and the cell pellets were gently resuspended with 50 \u00b5L 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10\u00d7Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10\u00d7Genomics Chromium Controller according to the manufacturer\u2019s manual for a target of 4 000 cells per sample.", null, "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\u2013/\u2013 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 \u00d7 rpm for 5 minutes at 4\u00b0C  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 \u00b5m membrane filter at 28.5\u00b0C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 \u00b5L 6\u00d7Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C. 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 \u00b5m pore cell strainer. post centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  the supernatant was removed  and the cell pellets were gently resuspended with 50 \u00b5L 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10\u00d7Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10\u00d7Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP521426", null, "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", null, "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\u2013/\u2013 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\u2013/\u2013 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", null, "pubmed:39499852", null, "WT  scRNAseq", "GSM8412847", null, "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\u00d7Genomics 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", null, "Five pituitaries were dissected from each gnrh3\u2013/\u2013 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 \u00d7 rpm for 5 minutes at 4\u00b0C  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 \u00b5m membrane filter at 28.5\u00b0C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 \u00b5L 6\u00d7Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C. 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 \u00b5m pore cell strainer. post centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  the supernatant was removed  and the cell pellets were gently resuspended with 50 \u00b5L 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10\u00d7Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10\u00d7Genomics Chromium Controller according to the manufacturer\u2019s manual for a target of 4 000 cells per sample.", null, "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\u2013/\u2013 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 \u00d7 rpm for 5 minutes at 4\u00b0C  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 \u00b5m membrane filter at 28.5\u00b0C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 \u00b5L 6\u00d7Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C. 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 \u00b5m pore cell strainer. post centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  the supernatant was removed  and the cell pellets were gently resuspended with 50 \u00b5L 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10\u00d7Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10\u00d7Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP521426", null, "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", null, "United States", "2024-07-22", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [33348, "SRR30085223", "SRX25558689", "SRS22210797", "SRP523634", "PRJNA1142970", "rna sequncing of POMC miR 7a zebrafish", "PRJNA1142970", "Other", null, null, null, null, null, "Pomc WT", null, "strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:5 mpf date:2017 03|geo loc name:Taiwan|sex:pooled male and female|tissue:Pituitary gland|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of pomc neuron:wild type zebrafish", "Pomc WT", "Pomc WT", "RNA was extracted from pooled zebrafish pomc neron", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", null, "SRP523634", null, null, "Pomc_WT_1.fq Pomc_WT_2.fq", "fastq fastq", 7525490700.0, 25084969.0, "Pomc WT 1.fq", "0:150 1:150", "A:2000028813;C:1750437540;G:1771219215;T:2003249941;N:555191", 150, 150, null, null, 2000028813, 1750437540, 1771219215, 2003249941, 555191, "SRX25558689", "SRS22210797", "SRA1937807", "National Yang Ming Chiao Tung University|Institute of Biopharmaceutical Sciences", "National Yang Ming Chiao Tung University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2024-08-01", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [33349, "SRR30085224", "SRX25558688", "SRS22210796", "SRP523634", "PRJNA1142970", "rna sequncing of POMC miR 7a zebrafish", "PRJNA1142970", "Other", null, null, null, null, null, "Pomc 7a", null, "strain:Pomc miR7a|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:5 mpf date:2017 03|geo loc name:Taiwan|sex:pooled male and female|tissue:Pituitary gland|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of pomc neuron:micorRNA 7a overexpressed zebrafish", "Pomc 7a", "Pomc 7a", "RNA was extracted from pooled zebrafish pomc neron", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", null, "SRP523634", null, null, "Pomc_7a_1.fq Pomc_7a_2.fq", "fastq fastq", 9785072700.0, 32616909.0, "Pomc 7a 1.fq", "0:150 1:150", "A:2643936280;C:2244968340;G:2260302975;T:2635083506;N:781599", 150, 150, null, null, 2643936280, 2244968340, 2260302975, 2635083506, 781599, "SRX25558688", "SRS22210796", "SRA1937807", "National Yang Ming Chiao Tung University|Institute of Biopharmaceutical Sciences", "National Yang Ming Chiao Tung University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2024-08-01", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [34324, "SRR31647630", "SRX27010714", "SRS23475005", "SRP550229", "PRJNA1195876", "Anti M\u00fcllerian 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 M\u00fcllerian 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.", null, "pubmed:40348785", null, "pituitary gland  Amh KO", "GSM8672964", null, "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", null, "post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer\u2019s 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 \u00b0C 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 \u03bcm cell strainer  centrifuged 2000 rpm  5 min  4 \u00b0C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3.1 according to the manufacturer\u2019s instructions.", null, "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 \u00b0C 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 \u03bcm cell strainer  centrifuged 2000 rpm  5 min  4 \u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP550229", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-12-09", "Undetermined", "Undetermined", "Pituitary Gland", "Endocrine System"], [34325, "SRR31647631", "SRX27010713", "SRS23475006", "SRP550229", "PRJNA1195876", "Anti M\u00fcllerian 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 M\u00fcllerian 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.", null, "pubmed:40348785", null, "pituitary gland  WT", "GSM8672963", null, "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", null, "post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer\u2019s 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 \u00b0C 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 \u03bcm cell strainer  centrifuged 2000 rpm  5 min  4 \u00b0C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3.1 according to the manufacturer\u2019s instructions.", null, "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 \u00b0C 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 \u03bcm cell strainer  centrifuged 2000 rpm  5 min  4 \u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP550229", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-12-09", "Undetermined", "Undetermined", "Pituitary Gland", "Endocrine System"], [44043, "SRR6237746", "SRX3345984", "SRS2646512", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate2 A6 AMCA", "GSM2836694", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "Sample Plate2 A6 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "GSM2836694", "GSM2836694: Sample Plate2 A6 AMCA; Danio rerio; RNA Seq", "GSM2836694", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836694", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate2_A6_AMCA_Neg.fastq.gz", "fastq", 1229895822.0, 20184545.0, "GSM2836694 r1", "0:60.93 1:0", "A:354923207;C:259144918;G:256606445;T:359057403;N:163849", 60, 0, null, null, 354923207, 259144918, 256606445, 359057403, 163849, "SRX3345984", "SRS2646512", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.87646, null, 0.26527, null, 0.8257, null, 0.55303, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44044, "SRR6237745", "SRX3345983", "SRS2646515", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate2 A5 AMCA", "GSM2836693", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "Sample Plate2 A5 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "GSM2836693", "GSM2836693: Sample Plate2 A5 AMCA; Danio rerio; RNA Seq", "GSM2836693", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836693", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate2_A5_AMCA_Pos.fastq.gz", "fastq", 925676587.0, 15189171.0, "GSM2836693 r1", "0:60.94 1:0", "A:282028510;C:179853567;G:179383383;T:284281435;N:129692", 60, 0, null, null, 282028510, 179853567, 179383383, 284281435, 129692, "SRX3345983", "SRS2646515", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.90747, null, 0.36422, null, 0.74215, null, 0.54419, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44045, "SRR6237744", "SRX3345982", "SRS2646511", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate2 A4 AMCA", "GSM2836692", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "Sample Plate2 A4 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "GSM2836692", "GSM2836692: Sample Plate2 A4 AMCA; Danio rerio; RNA Seq", "GSM2836692", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836692", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate2_A4_AMCA_Neg.fastq.gz", "fastq", 1160014329.0, 19037174.0, "GSM2836692 r1", "0:60.93 1:0", "A:339245851;C:240318483;G:237965388;T:342331066;N:153541", 60, 0, null, null, 339245851, 240318483, 237965388, 342331066, 153541, "SRX3345982", "SRS2646511", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.89175, null, 0.24416, null, 0.82384, null, 0.55389, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44046, "SRR6237743", "SRX3345981", "SRS2646513", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate2 A3 AMCA", "GSM2836691", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "Sample Plate2 A3 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "GSM2836691", "GSM2836691: Sample Plate2 A3 AMCA; Danio rerio; RNA Seq", "GSM2836691", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836691", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate2_A3_AMCA_Pos.fastq.gz", "fastq", 855655864.0, 14040472.0, "GSM2836691 r1", "0:60.94 1:0", "A:257233140;C:169854422;G:169238352;T:259211059;N:118891", 60, 0, null, null, 257233140, 169854422, 169238352, 259211059, 118891, "SRX3345981", "SRS2646513", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.90605, null, 0.30761, null, 0.74067, null, 0.55271, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44047, "SRR6237742", "SRX3345980", "SRS2646514", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate2 A2 AMCA", "GSM2836690", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "Sample Plate2 A2 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "GSM2836690", "GSM2836690: Sample Plate2 A2 AMCA; Danio rerio; RNA Seq", "GSM2836690", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836690", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate2_A2_AMCA_Neg.fastq.gz", "fastq", 1168909471.0, 19185392.0, "GSM2836690 r1", "0:60.93 1:0", "A:326281148;C:256738933;G:252744782;T:332989234;N:155374", 60, 0, null, null, 326281148, 256738933, 252744782, 332989234, 155374, "SRX3345980", "SRS2646514", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.88849, null, 0.1697, null, 0.86602, null, 0.52913, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44048, "SRR6237741", "SRX3345979", "SRS2646510", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate2 A1 AMCA", "GSM2836689", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "Sample Plate2 A1 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "GSM2836689", "GSM2836689: Sample Plate2 A1 AMCA; Danio rerio; RNA Seq", "GSM2836689", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836689", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate2_A1_AMCA_Pos.fastq.gz", "fastq", 915106129.0, 15016536.0, "GSM2836689 r1", "0:60.94 1:0", "A:271804923;C:184830364;G:184695096;T:273646193;N:129553", 60, 0, null, null, 271804923, 184830364, 184695096, 273646193, 129553, "SRX3345979", "SRS2646510", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.909, null, 0.28209, null, 0.74582, null, 0.54537, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44049, "SRR6237740", "SRX3345978", "SRS2646509", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate1 A8 AMCA", "GSM2836688", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "Sample Plate1 A8 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "GSM2836688", "GSM2836688: Sample Plate1 A8 AMCA; Danio rerio; RNA Seq", "GSM2836688", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836688", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate1_A8_AMCA_Neg.fastq.gz", "fastq", 1174636209.0, 19276749.0, "GSM2836688 r1", "0:60.94 1:0", "A:346218731;C:240547553;G:237863913;T:349847274;N:158738", 60, 0, null, null, 346218731, 240547553, 237863913, 349847274, 158738, "SRX3345978", "SRS2646509", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.89653, null, 0.29731, null, 0.82388, null, 0.57688, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44050, "SRR6237739", "SRX3345977", "SRS2646507", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate1 A7 AMCA", "GSM2836687", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "Sample Plate1 A7 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "GSM2836687", "GSM2836687: Sample Plate1 A7 AMCA; Danio rerio; RNA Seq", "GSM2836687", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836687", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate1_A7_AMCA_Pos.fastq.gz", "fastq", 919004945.0, 15079582.0, "GSM2836687 r1", "0:60.94 1:0", "A:281188323;C:177657384;G:177254638;T:282775426;N:129174", 60, 0, null, null, 281188323, 177657384, 177254638, 282775426, 129174, "SRX3345977", "SRS2646507", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.8999, null, 0.31855, null, 0.7643, null, 0.56856, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44051, "SRR6237738", "SRX3345976", "SRS2646506", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate1 A6 AMCA", "GSM2836686", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "Sample Plate1 A6 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Neg|cell type:non pituicytes", "GSM2836686", "GSM2836686: Sample Plate1 A6 AMCA; Danio rerio; RNA Seq", "GSM2836686", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836686", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate1_A6_AMCA_Neg.fastq.gz", "fastq", 1217567270.0, 19981819.0, "GSM2836686 r1", "0:60.93 1:0", "A:366468588;C:242252329;G:239380324;T:369298417;N:167612", 60, 0, null, null, 366468588, 242252329, 239380324, 369298417, 167612, "SRX3345976", "SRS2646506", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.87327, null, 0.29592, null, 0.86026, null, 0.61414, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [44052, "SRR6237737", "SRX3345975", "SRS2646508", "SRP123109", "PRJNA416462", "Transcriptome of zebrafish neurohypophyseal astroglia pituicytes", "GSE106371", "Transcriptome Analysis", "The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument", null, "pubmed:30449506", null, "Sample Plate1 A5 AMCA", "GSM2836685", null, "source name:hypophysis|strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "Sample Plate1 A5 AMCA", "cutadapt used to trim poly A and poly T   low quality and adapter fastq raw files submitted are post trimming Reads were mapped with TopHat v2.0.13 iGenomes Danio rerio UCSC danRer10 gene counts were calculated with HTSeq count parameters:  s no  t exon  m intersection strict  i gene id DESeq2 was used to normalize and detect differentially expressed genes AMCA+ versus AMCA  Genome build: danRer10 Supplementary files format and content: Output of HTSeq and DESeq2", "hypophysis", "Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM \u03b2 Ala Lys Ne AMCA Biotrend # BP0352. 3 hours post injection pituitaries were dissected as described in Toro et al.  Gene Expr Patterns 2009.", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "Adult zebrafish were raised and bred according to standard protocols.", "strain:TL|tissue:hypophysis|age:12 month|Sex:male|b ala lys ne amca labelling:Pos|cell type:pituicytes", "GSM2836685", "GSM2836685: Sample Plate1 A5 AMCA; Danio rerio; RNA Seq", "GSM2836685", null, "1", "Dissected pituitaries 5 groups; n= 7 per group were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250\u00b5L ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM Roche for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50\u00b5l of FBS and dissociated cells were pelleted by centrifuging at 500g at 4\u00b0C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer Leibovitz L 15 with 0.3mM Glutamine GIBCO  0.8mM CaCl2  Pen 50 U/mL + Strep 0.05/mL  FBS 1% and filtered with a 40 \u03bcm cell strainer BD Transduction Laboratories  San Jose  CA. Propidium iodide was added to label dead cells.  High speed FACS was performed using an SORP FACSAria machine BD  Bioscience  San Jose  CA with 70\u00b5m nozzle. A two gate FACS technique was used to select only AMCA+ cells from non fluorescent and auto fluorescent cells. As a control  non AMCA AMCA  cells were sorted. The cells were collected into a 384 well sterile plate filled with the 1X lysis buffer and RNAsin SMARTer Ultra Low Input RNA Kit for Sequencing   v3 Takara Bio USA  Inc. CA. The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at  80\u00b0C. Two independent FACS experiments were performed  yielding six samples 3 AMCA+ and 3 AMCA  from 3 groups and four samples 2 AMCA+ and 2 AMCA   from 2 groups. Samples were thawed  reverse transcribed and amplified to create full length transcriptome using the SMARTer\u00ae Ultra\u2122 Low Input RNA for Sequencing   v3 kit. Amplification was performed with 15 cycles. Following the amplification  clean up was done using Ampure XP beads Beckman Coulter. The amplified cDNA products were sheared by ultrasonicator Covaris E220X.  About 3ng of sheared  amplified cDNA from each sample were processed as previously described Blecher Gonen R. et al. Nat. Prot. 2013. Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18 22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.", "GEO Accession:GSM2836685", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP123109", null, null, "Sample_Plate1_A5_AMCA_Pos.fastq.gz", "fastq", 995781320.0, 16339491.0, "GSM2836685 r1", "0:60.94 1:0", "A:304872127;C:192446811;G:191928153;T:306392280;N:141949", 60, 0, null, null, 304872127, 192446811, 191928153, 306392280, 141949, "SRX3345975", "SRS2646508", "SRA626615", "GEO", "Bioinformatics Unit, Biological Services, Weizmann Institute of Science", 1, 0.90464, null, 0.36217, null, 0.74836, null, 0.56177, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Israel", "2017-10-31", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Transplant", "GSM4474605", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Male1", "GSM4474604", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [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.", null, "pubmed:33093109", null, "Males", "GSM4474603", null, "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", null, "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", null, "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", null, "SRP256300", null, null, "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, null, null, 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", null, "United States", "2020-04-13", "Adult", "Adult", "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.", null, "pubmed:37683631", null, "AB9278", "GSM6153483", null, "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 \u03b2 Ala Lys N\u03b5 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "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, null, null, 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, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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.", null, "pubmed:37683631", null, "AB9277", "GSM6153482", null, "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 \u03b2 Ala Lys N\u03b5 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "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, null, null, 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, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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.", null, "pubmed:37683631", null, "AB9280", "GSM6153481", null, "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 \u03b2 Ala Lys N\u03b5 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "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, null, null, 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, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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.", null, "pubmed:37683631", null, "AB9279", "GSM6153480", null, "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 \u03b2 Ala Lys N\u03b5 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "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, null, null, 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, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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.", null, "pubmed:37683631", null, "AB7418", "GSM6153479", null, "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 \u03b2 Ala Lys N\u03b5 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, null, "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, null, null, 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, null, 69, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "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.", null, "pubmed:37683631", null, "AB7417", "GSM6153478", null, "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 \u03b2 Ala Lys N\u03b5 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl 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 40\u03bcm 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, null, "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, null, null, 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, null, 69, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Juvenile", "Juvenile", "Pituitary Gland", "Endocrine System"]], "truncated": false, "filtered_table_rows_count": 34, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_selection\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "cDNA", "p1": "Pituitary Gland"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&tissue_curation=Pituitary+Gland", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 34, "toggle_url": 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