{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"unknown\" and tissue_curation_coarse = \"Endocrine System\"", "rows": [[10002, "ERR6806875", "ERX6430468", "ERS5060069", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish whole pancreas RNA seq replicate2 raw reads", "Zebrafish Whole Pancreas RNA seq replicate2", "SAMEA7301510", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301510|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate2|common name:zebrafish|sample name:Zebrafish Whole Pancreas RNA seq replicate2|tissue type:whole pancreas", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 6", "Exocrine2", "1", "Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Exocrine_Old_1.fastq.gz", "fastq", 1715678250.0, 34313565.0, "ena RUN I3S 23 09 2021 16:43:09:330 6", "0:50 1:0", "A:423211245;C:429948631;G:413857387;T:448546996;N:113991", 50, 0, null, null, 423211245, 429948631, 413857387, 448546996, 113991, "ERX6430468", "ERS5060069", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.94581, null, 0.03181, null, 0.80026, null, 0.48102, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [10003, "ERR6806874", "ERX6430467", "ERS5060068", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish whole pancreas RNA seq replicate1 raw reads", "Zebrafish Whole Pancreas RNA seq replicate1", "SAMEA7301509", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301509|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate1|common name:zebrafish|sample name:Zebrafish Whole Pancreas RNA seq replicate1|tissue type:whole pancreas", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 5", "Exocrine1", "1", "Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Exocrine_Young_1.fastq.gz", "fastq", 1751070500.0, 35021410.0, "ena RUN I3S 23 09 2021 16:43:09:330 5", "0:50 1:0", "A:412303526;C:454121976;G:438481251;T:446048184;N:115563", 50, 0, null, null, 412303526, 454121976, 438481251, 446048184, 115563, "ERX6430467", "ERS5060068", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.93968, null, 0.02618, null, 0.8003, null, 0.58539, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [10004, "ERR6806873", "ERX6430466", "ERS5060036", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish endocrine pancreas RNA seq replicate4 raw reads", "Zebrafish Endocrine Pancreas RNA seq replicate4", "SAMEA7301477", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301477|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate4|common name:zebrafish|sample name:Zebrafish Endocrine Pancreas RNA seq replicate4|tissue type:endocrine pancreas principal islet", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 4", "Endocrine4", "1", "Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Endocrine_Old_2.fastq.gz", "fastq", 1710560600.0, 34211212.0, "ena RUN I3S 23 09 2021 16:43:09:330 4", "0:50 1:0", "A:441527784;C:412091003;G:396100295;T:460728135;N:113383", 50, 0, null, null, 441527784, 412091003, 396100295, 460728135, 113383, "ERX6430466", "ERS5060036", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.95616, null, 0.04334, null, 0.84585, null, 0.17182, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [10005, "ERR6806872", "ERX6430465", "ERS5060035", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish endocrine pancreas RNA seq replicate3 raw reads", "Zebrafish Endocrine Pancreas RNA seq replicate3", "SAMEA7301476", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301476|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate3|common name:zebrafish|sample name:Zebrafish Endocrine Pancreas RNA seq replicate3|tissue type:endocrine pancreas principal islet", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 3", "Endocrine3", "1", "Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Endocrine_Old_1.fastq.gz", "fastq", 1979582750.0, 39591655.0, "ena RUN I3S 23 09 2021 16:43:09:330 3", "0:50 1:0", "A:483713055;C:499972514;G:479484600;T:516281513;N:131068", 50, 0, null, null, 483713055, 499972514, 479484600, 516281513, 131068, "ERX6430465", "ERS5060035", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.93722, null, 0.04096, null, 0.7559, null, 0.52069, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [10006, "ERR6806871", "ERX6430464", "ERS5060034", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate2", "Zebrafish Endocrine Pancreas RNA seq replicate2", "SAMEA7301475", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301475|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate2|common name:zebrafish|sample name:Zebrafish Endocrine Pancreas RNA seq replicate2|tissue type:endocrine pancreas principal islet", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:329 2", "Endocrine2", "1", "Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Endocrine_Young_2.fastq.gz", "fastq", 1846315600.0, 36926312.0, "ena RUN I3S 23 09 2021 16:43:09:329 2", "0:50 1:0", "A:466245839;C:453675875;G:433502059;T:492768958;N:122869", 50, 0, null, null, 466245839, 453675875, 433502059, 492768958, 122869, "ERX6430464", "ERS5060034", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.93566, null, 0.06945, null, 0.74065, null, 0.47497, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [10007, "ERR6806870", "ERX6430463", "ERS5060033", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate1", "Zebrafish Endocrine Pancreas RNA seq replicate1", "SAMEA7301474", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301474|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate1|common name:zebrafish|sample name:Zebrafish Endocrine Pancreas RNA seq replicate1|tissue type:endocrine pancreas principal islet", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:329 1", "Endocrine1", "1", "Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Endocrine_Young_1.fastq.gz", "fastq", 1331184450.0, 26623689.0, "ena RUN I3S 23 09 2021 16:43:09:329 1", "0:50 1:0", "A:336761837;C:326693218;G:311881921;T:355763246;N:84228", 50, 0, null, null, 336761837, 326693218, 311881921, 355763246, 84228, "ERX6430463", "ERS5060033", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.93154, null, 0.07422, null, 0.73064, null, 0.53917, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [39917, "SRR2353210", "SRX1225282", "SRS1065171", "SRP063624", "PRJNA295427", "Expression profiling of centroacinar cells from adult zebrafish pancreas", "GSE72963", "Transcriptome Analysis", "We sequenced mRNA from two preparations of isolated Notch responsive ductal pancreas cells and compared transcript expression to all other non Notch responsive cells from each sample to charactarize zebrafish centroacinar cells. 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Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.", null, "pubmed:26153247", null, "CAC rep 2", "GSM1875474", null, "source name:pancreas CAC|tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated centroacinar cells", "CAC rep 2", "Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values", "pancreas CAC", null, "Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. 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Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.", null, "pubmed:26153247", null, "non CAC rep 1", "GSM1875473", null, "source name:pancreas non CAC|tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated non centroacinar cells", "non CAC rep 1", "Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values", "pancreas non CAC", null, "Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols", null, "tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated non centroacinar cells", "GSM1875473", "GSM1875473: non CAC rep 1; Danio rerio; RNA Seq", "GSM1875473", null, "1", "Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols", "GEO Accession:GSM1875473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP063624", null, null, "H0J49ADXXs_1_2_merged.fastq.bz2", "fastq", 8167909125.0, 108905455.0, "GSM1875473 r1", "0:75", "A:2352532315;C:1630885687;G:1811590860;T:2358426654;N:14473609", 75, null, null, null, 2352532315, 1630885687, 1811590860, 2358426654, 14473609, "SRX1225280", "SRS1065173", "SRA297337", "GEO", "Institute of Genetic Medicine, Johns Hopkins University", 1, 0.56456, null, 0.17736, null, 0.74525, null, 0.57983, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-11", "Adult", "Adult", "Pancreas", "Endocrine System"], [39920, "SRR2353207", "SRX1225279", "SRS1065174", "SRP063624", "PRJNA295427", "Expression profiling of centroacinar cells from adult zebrafish pancreas", "GSE72963", "Transcriptome Analysis", "We sequenced mRNA from two preparations of isolated Notch responsive ductal pancreas cells and compared transcript expression to all other non Notch responsive cells from each sample to charactarize zebrafish centroacinar cells. Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.", null, "pubmed:26153247", null, "CAC rep 1", "GSM1875472", null, "source name:pancreas CAC|tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated centroacinar cells", "CAC rep 1", "Reads were processed and mapped to Zv9/danRer7 using RSEM EBseq was used to determine differential expression and significance values Genome build: Zv9/danRer7 Supplementary files format and content: tab delimited text files using corrected and uncorrected foldchange values", "pancreas CAC", null, "Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols", null, "tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated centroacinar cells", "GSM1875472", "GSM1875472: CAC rep 1; Danio rerio; RNA Seq", "GSM1875472", null, "1", "Pancreas was dissected on ice and dissociated. CACs and non CACs were sorted by FACS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used for the construction of sequencing libraries. Libraries were constructed using standard Illumina protocols", "GEO Accession:GSM1875472", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP063624", null, null, "H0J49ADXXs_1_1_merged.fastq.bz2", "fastq", 8167909125.0, 108905455.0, "GSM1875472 r1", "0:75", "A:2418955841;C:1674627530;G:1764871153;T:2308386909;N:1067692", 75, null, null, null, 2418955841, 1674627530, 1764871153, 2308386909, 1067692, "SRX1225279", "SRS1065174", "SRA297337", "GEO", "Institute of Genetic Medicine, Johns Hopkins University", 1, 0.66215, null, 0.21771, null, 0.72437, null, 0.57789, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-11", "Adult", "Adult", "Pancreas", "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"], [50713, "SRR8255922", "SRX5073702", "SRS4087528", "SRP171016", "PRJNA507363", "Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection", "GSE123036", "Transcriptome Analysis", "To assess the effect of chronic inflammation on the beta cells transcriptome  we conducted RNA sequencing  from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode.  method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs  were generated by deep sequencing  in duplicate  using llumina HiSeq2500.", null, "pubmed:30679186", null, "Il1B rep2", "GSM3494234", null, "source name:Pancreatic beta cells|genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells", "Il1B rep2", "Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zebrafish genome GRCz10  using GSNAP from Ensembl gene annotation  version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Pancreatic beta cells", null, "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells", "GSM3494234", "GSM3494234: Il1B rep2; Danio rerio; RNA Seq", "GSM3494234", null, "1", "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3494234", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP171016", null, null, "L19371_Track-47496_R1.fastq.gz", "fastq", 3282305632.0, 43188232.0, "GSM3494234 r1", "0:76 1:0", "A:961171458;C:699797228;G:707162172;T:914140351;N:34423", 76, 0, null, null, 961171458, 699797228, 707162172, 914140351, 34423, "SRX5073702", "SRS4087528", "SRA815642", "GEO", "Ninov, CRTD", 1, 0.88789, null, 0.19663, null, 0.77461, null, 0.56289, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2018-11-28", "Adult", "Adult", "Pancreas", "Endocrine System"], [50714, "SRR8255921", "SRX5073701", "SRS4087527", "SRP171016", "PRJNA507363", "Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection", "GSE123036", "Transcriptome Analysis", "To assess the effect of chronic inflammation on the beta cells transcriptome  we conducted RNA sequencing  from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode.  method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs  were generated by deep sequencing  in duplicate  using llumina HiSeq2500.", null, "pubmed:30679186", null, "Il1B rep1", "GSM3494233", null, "source name:Pancreatic beta cells|genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells", "Il1B rep1", "Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zebrafish genome GRCz10  using GSNAP from Ensembl gene annotation  version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Pancreatic beta cells", null, "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells", "GSM3494233", "GSM3494233: Il1B rep1; Danio rerio; RNA Seq", "GSM3494233", null, "1", "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3494233", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP171016", null, null, "L19370_Track-47495_R1.fastq.gz", "fastq", 3117378488.0, 41018138.0, "GSM3494233 r1", "0:76 1:0", "A:900337994;C:672684479;G:688186415;T:856137569;N:32031", 76, 0, null, null, 900337994, 672684479, 688186415, 856137569, 32031, "SRX5073701", "SRS4087527", "SRA815642", "GEO", "Ninov, CRTD", 1, 0.88054, null, 0.16457, null, 0.7735, null, 0.55887, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2018-11-28", "Adult", "Adult", "Pancreas", "Endocrine System"], [50715, "SRR8255920", "SRX5073700", "SRS4087526", "SRP171016", "PRJNA507363", "Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection", "GSE123036", "Transcriptome Analysis", "To assess the effect of chronic inflammation on the beta cells transcriptome  we conducted RNA sequencing  from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode.  method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs  were generated by deep sequencing  in duplicate  using llumina HiSeq2500.", null, "pubmed:30679186", null, "Con rep2", "GSM3494232", null, "source name:Pancreatic beta cells|genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type", "Con rep2", "Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zebrafish genome GRCz10  using GSNAP from Ensembl gene annotation  version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Pancreatic beta cells", null, "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type", "GSM3494232", "GSM3494232: Con rep2; Danio rerio; RNA Seq", "GSM3494232", null, "1", "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3494232", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP171016", null, null, "L19373_Track-47629_R1.fastq.gz", "fastq", 3896547512.0, 51270362.0, "GSM3494232 r1", "0:76", "A:1137736314;C:843105511;G:852627922;T:1062822946;N:254819", 76, null, null, null, 1137736314, 843105511, 852627922, 1062822946, 254819, "SRX5073700", "SRS4087526", "SRA815642", "GEO", "Ninov, CRTD", 1, 0.86977, null, 0.16515, null, 0.77078, null, 0.40368, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2018-11-28", "Adult", "Adult", "Pancreas", "Endocrine System"], [50716, "SRR8255919", "SRX5073699", "SRS4087525", "SRP171016", "PRJNA507363", "Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection", "GSE123036", "Transcriptome Analysis", "To assess the effect of chronic inflammation on the beta cells transcriptome  we conducted RNA sequencing  from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode.  method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs  were generated by deep sequencing  in duplicate  using llumina HiSeq2500.", null, "pubmed:30679186", null, "Con rep1", "GSM3494231", null, "source name:Pancreatic beta cells|genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type", "Con rep1", "Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zebrafish genome GRCz10  using GSNAP from Ensembl gene annotation  version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Pancreatic beta cells", null, "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type", "GSM3494231", "GSM3494231: Con rep1; Danio rerio; RNA Seq", "GSM3494231", null, "1", "Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation  islets were collected in PBS chilled on ice. post one washing with ice cold PBS  islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 with 0.1% Pluronic F 68 ThermoFisher  24040032 at 37\u02daC in a benchtop shaker set at 350 rpm for 50 min. Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4\u02daC. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+  Mg2++0.1% Pluronic F 68. To remove debris  the solution was passed over a 30 mm cell filter Miltenyi Biotec  130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3494231", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP171016", null, null, "L19372_Track-47628_R1.fastq.gz", "fastq", 3743010792.0, 49250142.0, "GSM3494231 r1", "0:76", "A:1081119100;C:816543927;G:821868656;T:1023236057;N:243052", 76, null, null, null, 1081119100, 816543927, 821868656, 1023236057, 243052, "SRX5073699", "SRS4087525", "SRA815642", "GEO", "Ninov, CRTD", 1, 0.87612, null, 0.16984, null, 0.7684, null, 0.57882, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2018-11-28", "Adult", "Adult", "Pancreas", "Endocrine System"], [64122, "SRR14272168", "SRX10633820", "SRS8730202", "SRP315319", "PRJNA722925", "Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation", "PRJNA722925", "Other", "Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.", null, null, null, "Pancreas islets   Pancreas islet 6dpf B2", "Pancreas islets   Islet 6d B2 AGN000787", null, "strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000684|replicate ref:AGN000787|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Pancreas islets   Pancreas islet 6dpf B2", "AGR001074", "AGR001074", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP315319", null, null, "AGR001074_R1.fastq.gz", "fastq", 467368080.0, 6149580.0, "AGR001074 R1.fastq.gz", "0:76 1:0", "A:144866246;C:90980862;G:90828673;T:140671264;N:21035", 76, 0, null, null, 144866246, 90980862, 90828673, 140671264, 21035, "SRX10633820", "SRS8730202", "SRA1220217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.86223, null, 0.47625, null, 0.68556, null, 0.52132, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-04-19", "Larval", "Larval", "Pancreas", "Endocrine System"], [64123, "SRR14272169", "SRX10633819", "SRS8730201", "SRP315319", "PRJNA722925", "Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation", "PRJNA722925", "Other", "Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.", null, null, null, "Pancreas islets   Pancreas islet 6dpf B1", "Pancreas islets   Islet 6d B1 AGN000786", null, "strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000684|replicate ref:AGN000786|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Pancreas islets   Pancreas islet 6dpf B1", "AGR001073", "AGR001073", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP315319", null, null, "AGR001073_R1.fastq.gz", "fastq", 592506792.0, 7796142.0, "AGR001073 R1.fastq.gz", "0:76 1:0", "A:179281934;C:120318002;G:119990438;T:172891644;N:24774", 76, 0, null, null, 179281934, 120318002, 119990438, 172891644, 24774, "SRX10633819", "SRS8730201", "SRA1220217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.84252, null, 0.35277, null, 0.69219, null, 0.54723, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-04-19", "Larval", "Larval", "Pancreas", "Endocrine System"], [64128, "SRR14272174", "SRX10633814", "SRS8730196", "SRP315319", "PRJNA722925", "Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation", "PRJNA722925", "Other", "Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.", null, null, null, "Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2", "Pancreas islets   Islet SST b cell abt 4d B2 AGN000782", null, "strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000680|replicate ref:AGN000782|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2", "AGR001070", "AGR001070", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP315319", null, null, "AGR001070_R1.fastq.gz", "fastq", 481320616.0, 6333166.0, "AGR001070 R1.fastq.gz", "0:76 1:0", "A:151409804;C:91026556;G:90673968;T:148189727;N:20561", 76, 0, null, null, 151409804, 91026556, 90673968, 148189727, 20561, "SRX10633814", "SRS8730196", "SRA1220217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.82954, null, 0.59765, null, 0.75538, null, 0.53049, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-04-19", "Larval", "Larval", "Pancreas", "Endocrine System"], [64129, "SRR14272175", "SRX10633813", "SRS8730195", "SRP315319", "PRJNA722925", "Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation", "PRJNA722925", "Other", "Diabetes can be caused by an insufficiency in beta cell mass. Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. 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Here  we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid  stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets  showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets  the increased beta cell differentiation originated from ductal cells. Mechanistically  comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine  carnitine  and serine pathways. 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