rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
321,ERR977589,ERX1054572,ERS805778,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Delta cells R3,SAMEA3498629,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498629|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:34|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:34,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 14,Delta R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B176_SSTcells-03122013_CAGATC_L001_R1_001.fastq.gz NGS14-B176_SSTcells-03122013_CAGATC_L001_R2_001.fastq.gz,fastq fastq,17691597128.0,87582164.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 14,0:101 1:101,A:4843643109;C:3683816237;G:3736882877;T:5332210638;N:95044267,101,101,,,4843643109,3683816237,3736882877,5332210638,95044267,ERX1054572,ERS805778,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.92685,0.84146,0.10249,0.11723,0.76532,0.78309,0.39721,0.43714,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
330,ERR977580,ERX1054563,ERS805769,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R3,SAMEA3498620,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498620|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:25|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:25,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 5,Beta R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B174_Betacells-03122013_GCCAAT_L002_R1_001.fastq.gz NGS14-B174_Betacells-03122013_GCCAAT_L002_R2_001.fastq.gz,fastq fastq,17625660086.0,87255743.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 5,0:101 1:101,A:4840276660;C:3724973884;G:3755195525;T:5214977933;N:90236084,101,101,,,4840276660,3724973884,3755195525,5214977933,90236084,ERX1054563,ERS805769,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90631,0.8718,0.11791,0.11942,0.76203,0.77638,0.53654,0.49457,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
331,ERR977579,ERX1054562,ERS805768,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R2 2,SAMEA3498619,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498619|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:24|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:24,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 4,Beta R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell2_A026_ATGTCA_L004_R1_001.fastq.gz BetaCell2_A026_ATGTCA_L004_R2_001.fastq.gz,fastq fastq,8532015198.0,42237699.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 4,0:101 1:101,A:2314776471;C:1823939144;G:1839244845;T:2552984556;N:1070182,101,101,,,2314776471,1823939144,1839244845,2552984556,1070182,ERX1054562,ERS805768,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.69844,0.57999,0.09124,0.07501,0.80876,0.82964,0.56023,0.5159,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
332,ERR977578,ERX1054561,ERS805767,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R2 1,SAMEA3498618,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498618|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:23|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:23,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 3,Beta R2 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell_ATGTCA_L005_R1_001.fastq.gz BetaCell_ATGTCA_L005_R2_001.fastq.gz,fastq fastq,3250611068.0,16092134.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 3,0:101 1:101,A:854826460;C:691024995;G:695294721;T:954934438;N:54530454,101,101,,,854826460,691024995,695294721,954934438,54530454,ERX1054561,ERS805767,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.67496,0.53873,0.08771,0.06606,0.80969,0.83433,0.56231,0.51717,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
333,ERR977577,ERX1054560,ERS805766,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R1 2,SAMEA3498617,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498617|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:22|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:22,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 2,Beta R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell1_A003_GTCCGC_L004_R1_001.fastq.gz BetaCell1_A003_GTCCGC_L004_R2_001.fastq.gz,fastq fastq,3765102038.0,18639119.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 2,0:101 1:101,A:1050226787;C:789381360;G:801049952;T:1123973291;N:470648,101,101,,,1050226787,789381360,801049952,1123973291,470648,ERX1054560,ERS805766,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90456,0.86125,0.12934,0.13194,0.77721,0.79109,0.56708,0.53213,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
334,ERR977576,ERX1054559,ERS805765,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R1 1,SAMEA3498616,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498616|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:21|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:21,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:486 1,Beta R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCells_30000_GTCCGC_L008_R1_001.fastq.gz BetaCells_30000_GTCCGC_L008_R2_001.fastq.gz,fastq fastq,10597717092.0,52463946.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:486 1,0:101 1:101,A:2951812422;C:2213949786;G:2252957090;T:3178649938;N:347856,101,101,,,2951812422,2213949786,2252957090,3178649938,347856,ERX1054559,ERS805765,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90302,0.84857,0.12843,0.12749,0.77745,0.79157,0.56129,0.52011,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
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,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,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,,,423211245,429948631,413857387,448546996,113991,ERX6430468,ERS5060069,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.94581,,0.03181,,0.80026,,0.48102,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,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,,,412303526,454121976,438481251,446048184,115563,ERX6430467,ERS5060068,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.93968,,0.02618,,0.8003,,0.58539,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,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,,,441527784,412091003,396100295,460728135,113383,ERX6430466,ERS5060036,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.95616,,0.04334,,0.84585,,0.17182,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,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,,,483713055,499972514,479484600,516281513,131068,ERX6430465,ERS5060035,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.93722,,0.04096,,0.7559,,0.52069,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,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,,,466245839,453675875,433502059,492768958,122869,ERX6430464,ERS5060034,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.93566,,0.06945,,0.74065,,0.47497,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,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,,,,,,,,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,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,,,336761837,326693218,311881921,355763246,84228,ERX6430463,ERS5060033,ERA6385885,I3S|European Nucleotide Archive,I3S,1,0.93154,,0.07422,,0.73064,,0.53917,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2020-09-11,Adult,Adult,Pancreas,Endocrine System
33348,SRR30085223,SRX25558689,SRS22210797,SRP523634,PRJNA1142970,rna sequncing of POMC miR 7a zebrafish,PRJNA1142970,Other,,,,,,Pomc WT,,strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:5 mpf date:2017 03|geo loc name:Taiwan|sex:pooled male and female|tissue:Pituitary gland|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of pomc neuron:wild type zebrafish,Pomc WT,Pomc WT,RNA was extracted from pooled zebrafish pomc neron,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiScanSQ,,SRP523634,,,Pomc_WT_1.fq Pomc_WT_2.fq,fastq fastq,7525490700.0,25084969.0,Pomc WT 1.fq,0:150 1:150,A:2000028813;C:1750437540;G:1771219215;T:2003249941;N:555191,150,150,,,2000028813,1750437540,1771219215,2003249941,555191,SRX25558689,SRS22210797,SRA1937807,National Yang Ming Chiao Tung University|Institute of Biopharmaceutical Sciences,National Yang Ming Chiao Tung University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Taiwan,2024-08-01,Adult,Adult,Pituitary Gland,Endocrine System
33349,SRR30085224,SRX25558688,SRS22210796,SRP523634,PRJNA1142970,rna sequncing of POMC miR 7a zebrafish,PRJNA1142970,Other,,,,,,Pomc 7a,,strain:Pomc miR7a|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:5 mpf date:2017 03|geo loc name:Taiwan|sex:pooled male and female|tissue:Pituitary gland|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of pomc neuron:micorRNA 7a overexpressed zebrafish,Pomc 7a,Pomc 7a,RNA was extracted from pooled zebrafish pomc neron,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiScanSQ,,SRP523634,,,Pomc_7a_1.fq Pomc_7a_2.fq,fastq fastq,9785072700.0,32616909.0,Pomc 7a 1.fq,0:150 1:150,A:2643936280;C:2244968340;G:2260302975;T:2635083506;N:781599,150,150,,,2643936280,2244968340,2260302975,2635083506,781599,SRX25558688,SRS22210796,SRA1937807,National Yang Ming Chiao Tung University|Institute of Biopharmaceutical Sciences,National Yang Ming Chiao Tung University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Taiwan,2024-08-01,Adult,Adult,Pituitary Gland,Endocrine System
36546,SRR4469353,SRX2278278,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Control for deltaCLK experiment   pineal gland CT14b,Control for deltaCLK experiment   pineal gland CT14b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,cont-7_AGTTCC_L001_R1_001.fastq.gz cont-7_AGTTCC_L001_R2_001.fastq.gz cont-7_AGTTCC_L002_R1_001.fastq.gz cont-7_AGTTCC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1478016300.0,14780163.0,Control for deltaCLK experiment   pineal gland CT14b run,0:50 1:50,A:371860402;C:353565906;G:345517418;T:383732200;N:23340374,50,50,,,371860402,353565906,345517418,383732200,23340374,SRX2278278,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90906,0.91515,0.20116,0.19445,0.72916,0.72835,0.49173,0.54608,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36547,SRR4469352,SRX2278277,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Control for deltaCLK experiment   pineal gland CT2,Control for deltaCLK experiment   pineal gland CT2,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,cont-4_AGTCAA_L001_R1_001.fastq.gz cont-4_AGTCAA_L001_R2_001.fastq.gz cont-4_AGTCAA_L002_R1_001.fastq.gz cont-4_AGTCAA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1470782400.0,14707824.0,Control for deltaCLK experiment   pineal gland CT2 run,0:50 1:50,A:391260359;C:331926713;G:321564174;T:402261946;N:23769208,50,50,,,391260359,331926713,321564174,402261946,23769208,SRX2278277,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89527,0.90214,0.13737,0.13571,0.68087,0.68051,0.4788,0.49087,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36548,SRR4469348,SRX2278239,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT22b,aanat2 deltaCLK pineal gland CT22b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-9_GATCAG_L001_R1_001.fastq.gz dclk-9_GATCAG_L001_R2_001.fastq.gz dclk-9_GATCAG_L002_R1_001.fastq.gz dclk-9_GATCAG_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1230723800.0,12307238.0,aanat2 deltaCLK pineal gland CT22b run,0:50 1:50,A:326116345;C:279149077;G:272739998;T:331989387;N:20728993,50,50,,,326116345,279149077,272739998,331989387,20728993,SRX2278239,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90153,0.90798,0.12705,0.12581,0.69238,0.69124,0.45781,0.47401,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36549,SRR4469008,SRX2278238,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT18b,aanat2 deltaCLK pineal gland CT18b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-8_ACTTGA_L001_R1_001.fastq.gz dclk-8_ACTTGA_L001_R2_001.fastq.gz dclk-8_ACTTGA_L002_R1_001.fastq.gz dclk-8_ACTTGA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,954886200.0,9548862.0,aanat2 deltaCLK pineal gland CT18b run,0:50 1:50,A:254282649;C:215854100;G:209622359;T:259594152;N:15532940,50,50,,,254282649,215854100,209622359,259594152,15532940,SRX2278238,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90085,0.90415,0.14674,0.14451,0.68874,0.68856,0.47777,0.49043,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36550,SRR4468783,SRX2278237,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT14b,aanat2 deltaCLK pineal gland CT14b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-7_CAGATC_L001_R1_001.fastq.gz dclk-7_CAGATC_L001_R2_001.fastq.gz dclk-7_CAGATC_L002_R1_001.fastq.gz dclk-7_CAGATC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1513650800.0,15136508.0,aanat2 deltaCLK pineal gland CT14b run,0:50 1:50,A:397790485;C:347226977;G:333623071;T:410528680;N:24481587,50,50,,,397790485,347226977,333623071,410528680,24481587,SRX2278237,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90378,0.90956,0.13414,0.13161,0.67927,0.67823,0.45986,0.47098,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36551,SRR4469351,SRX2278236,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT10b,aanat2 deltaCLK pineal gland CT10b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-12_CTTGTA_L001_R1_001.fastq.gz dclk-12_CTTGTA_L001_R2_001.fastq.gz dclk-12_CTTGTA_L002_R1_001.fastq.gz dclk-12_CTTGTA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1542083900.0,15420839.0,aanat2 deltaCLK pineal gland CT10b run,0:50 1:50,A:414372159;C:345091361;G:330865131;T:426545033;N:25210216,50,50,,,414372159,345091361,330865131,426545033,25210216,SRX2278236,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89601,0.90164,0.1494,0.14679,0.68509,0.68249,0.46593,0.47633,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36552,SRR4469350,SRX2278235,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT6b,aanat2 deltaCLK pineal gland CT6b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-11_GGCTAC_L001_R1_001.fastq.gz dclk-11_GGCTAC_L001_R2_001.fastq.gz dclk-11_GGCTAC_L002_R1_001.fastq.gz dclk-11_GGCTAC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1470018300.0,14700183.0,aanat2 deltaCLK pineal gland CT6b run,0:50 1:50,A:390422751;C:333175699;G:322905954;T:399684708;N:23829188,50,50,,,390422751,333175699,322905954,399684708,23829188,SRX2278235,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90133,0.90669,0.13486,0.13298,0.6802,0.67994,0.46476,0.47663,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36553,SRR4469349,SRX2278234,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT2b,aanat2 deltaCLK pineal gland CT2b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-10_TAGCTT_L001_R1_001.fastq.gz dclk-10_TAGCTT_L001_R2_001.fastq.gz dclk-10_TAGCTT_L002_R1_001.fastq.gz dclk-10_TAGCTT_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1322705100.0,13227051.0,aanat2 deltaCLK pineal gland CT2b run,0:50 1:50,A:353320808;C:296680969;G:289897303;T:360502140;N:22303880,50,50,,,353320808,296680969,289897303,360502140,22303880,SRX2278234,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89935,0.90337,0.138,0.13471,0.68761,0.68615,0.44537,0.48064,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36554,SRR4468779,SRX2278233,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT22,aanat2 deltaCLK pineal gland CT22,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-3_TTAGGC_L001_R1_001.fastq.gz dclk-3_TTAGGC_L001_R2_001.fastq.gz dclk-3_TTAGGC_L002_R1_001.fastq.gz dclk-3_TTAGGC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1391437700.0,13914377.0,aanat2 deltaCLK pineal gland CT22 run,0:50 1:50,A:370600600;C:314791162;G:302422949;T:380945528;N:22677461,50,50,,,370600600,314791162,302422949,380945528,22677461,SRX2278233,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90077,0.90663,0.13303,0.12983,0.68176,0.67927,0.46884,0.48222,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36555,SRR4468778,SRX2278232,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT18,aanat2 deltaCLK pineal gland CT18,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-2_CGATGT_L001_R1_001.fastq.gz dclk-2_CGATGT_L001_R2_001.fastq.gz dclk-2_CGATGT_L002_R1_001.fastq.gz dclk-2_CGATGT_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1566024800.0,15660248.0,aanat2 deltaCLK pineal gland CT18 run,0:50 1:50,A:419409692;C:351933648;G:338078927;T:431073653;N:25528880,50,50,,,419409692,351933648,338078927,431073653,25528880,SRX2278232,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.9,0.90492,0.13189,0.12932,0.68757,0.68743,0.45253,0.4674,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36556,SRR4468777,SRX2278214,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT14,aanat2 deltaCLK pineal gland CT14,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-1_ATCACG_L001_R1_001.fastq.gz dclk-1_ATCACG_L001_R2_001.fastq.gz dclk-1_ATCACG_L002_R1_001.fastq.gz dclk-1_ATCACG_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1072983800.0,10729838.0,aanat2 deltaCLK pineal gland CT14 run,0:50 1:50,A:285412675;C:241757167;G:239216359;T:289121128;N:17476471,50,50,,,285412675,241757167,239216359,289121128,17476471,SRX2278214,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90548,0.91142,0.13613,0.13179,0.69808,0.69718,0.48357,0.48784,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36557,SRR4468782,SRX2278111,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT10,aanat2 deltaCLK pineal gland CT10,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-6_GCCAAT_L001_R1_001.fastq.gz dclk-6_GCCAAT_L001_R2_001.fastq.gz dclk-6_GCCAAT_L002_R1_001.fastq.gz dclk-6_GCCAAT_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1396334700.0,13963347.0,aanat2 deltaCLK pineal gland CT10 run,0:50 1:50,A:372017545;C:315699006;G:305209850;T:380695969;N:22712330,50,50,,,372017545,315699006,305209850,380695969,22712330,SRX2278111,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90165,0.90375,0.13729,0.13572,0.68901,0.68887,0.47627,0.48756,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36558,SRR4468781,SRX2278008,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT6,aanat2 deltaCLK pineal gland CT6,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-5_ACAGTG_L001_R1_001.fastq.gz dclk-5_ACAGTG_L001_R2_001.fastq.gz dclk-5_ACAGTG_L002_R1_001.fastq.gz dclk-5_ACAGTG_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1400816900.0,14008169.0,aanat2 deltaCLK pineal gland CT6 run,0:50 1:50,A:372340894;C:317777109;G:301897255;T:386068427;N:22733215,50,50,,,372340894,317777109,301897255,386068427,22733215,SRX2278008,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89908,0.9022,0.14682,0.14409,0.68012,0.67795,0.46353,0.47947,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36559,SRR4468780,SRX2277943,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT2,aanat2 deltaCLK pineal gland CT2,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2:EGFP fish] were run on a single flow cell of an Illumina HiSeq2500 machine rapid run mode using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy.  Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-4_TGACCA_L001_R1_001.fastq.gz dclk-4_TGACCA_L001_R2_001.fastq.gz dclk-4_TGACCA_L002_R1_001.fastq.gz dclk-4_TGACCA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1507598800.0,15075988.0,aanat2 deltaCLK pineal gland CT2 run,0:50 1:50,A:401061420;C:339329123;G:332045345;T:410675395;N:24487517,50,50,,,401061420,339329123,332045345,410675395,24487517,SRX2277943,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90388,0.90981,0.12413,0.12289,0.68572,0.68532,0.47663,0.48902,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36563,SRR1048063,SRX363286,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark replica 3,Pineal gland dark R3,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For mRNA seq  pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen. library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall  6 libraries 3 light groups and 3 dark groups were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. On average  6.7 million paired end reads were obtained for each library. The reads were of 2x100 base pairs.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,d3_pineal_CAGATC_L002_R2_001.fastq d3_pineal_CAGATC_L002_R1_001.fastq,fastq fastq,1947522800.0,9737614.0,Pineal gland dark R3 run,0:101 1:99,A:510547277;C:456462539;G:450297233;T:513101663;N:17114088,101,99,,,510547277,456462539,450297233,513101663,17114088,SRX363286,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.92352,0.91715,0.10879,0.10898,0.6873,0.69023,0.48478,0.48106,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36564,SRR1048062,SRX363285,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark replica 2,Pineal gland dark R2,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For mRNA seq  pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen. library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall  6 libraries 3 light groups and 3 dark groups were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. On average  6.7 million paired end reads were obtained for each library. The reads were of 2x100 base pairs.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,d2_pineal_GCCAAT_L002_R2_001.fastq d2_pineal_GCCAAT_L002_R1_001.fastq,fastq fastq,1484149600.0,7420748.0,Pineal gland dark R2 run,0:101 1:99,A:385426867;C:351549544;G:346126979;T:388075322;N:12970888,101,99,,,385426867,351549544,346126979,388075322,12970888,SRX363285,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.92222,0.91476,0.10962,0.11121,0.68933,0.69359,0.48718,0.48244,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36565,SRR1048061,SRX363284,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark replica 1,Pineal gland dark R1,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For mRNA seq  pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen. library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall  6 libraries 3 light groups and 3 dark groups were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. On average  6.7 million paired end reads were obtained for each library. The reads were of 2x100 base pairs.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,d1_pineal_ACAGTG_L002_R1_001.fastq d1_pineal_ACAGTG_L002_R2_001.fastq,fastq fastq,1750757800.0,8753789.0,Pineal gland dark R1 run,0:101 1:99,A:458721893;C:411677417;G:404111686;T:460844026;N:15402778,101,99,,,458721893,411677417,404111686,460844026,15402778,SRX363284,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91494,0.90596,0.11581,0.11538,0.69248,0.69481,0.4833,0.47732,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36566,SRR1048060,SRX363283,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light replica 3,Pineal gland light R3,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For mRNA seq  pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen. library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall  6 libraries 3 light groups and 3 dark groups were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. On average  6.7 million paired end reads were obtained for each library. The reads were of 2x100 base pairs.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,l3_pineal_TGACCA_L002_R1_001.fastq l3_pineal_TGACCA_L002_R2_001.fastq,fastq fastq,1690222600.0,8451113.0,Pineal gland light R3 run,0:101 1:99,A:442363790;C:397493201;G:390948371;T:444488446;N:14928792,101,99,,,442363790,397493201,390948371,444488446,14928792,SRX363283,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91881,0.91058,0.11743,0.11843,0.69629,0.69923,0.48757,0.48035,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-13,Adult,Adult,Pineal Gland,Endocrine System
36567,SRR1048059,SRX363282,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light replica 2,Pineal gland light R2,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For mRNA seq  pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen. library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall  6 libraries 3 light groups and 3 dark groups were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. On average  6.7 million paired end reads were obtained for each library. The reads were of 2x100 base pairs.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,l2_pineal_TTAGGC_L002_R2_001.fastq l2_pineal_TTAGGC_L002_R1_001.fastq,fastq fastq,1014564400.0,5072822.0,Pineal gland light R2 run,0:101 1:99,A:276724352;C:226950331;G:223973268;T:276923072;N:9993377,101,99,,,276724352,226950331,223973268,276923072,9993377,SRX363282,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90704,0.90364,0.13141,0.13204,0.68688,0.69061,0.48164,0.48436,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36568,SRR1048058,SRX363281,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light replica 1,Pineal gland light R1,1,Adult 0.5 1.5 years old Tgaanat2:EGFP zebrafish Gothilf et al.  2002 were raised in a temperature controlled recirculation water system under 12 hr light: 12 hr dark LD cycles  and transferred to constant darkness DD at the end of the day prior to the experiment. Fish were exposed to a 1 hr light pulse light intensity of 12 W/m2 prior to sampling light treatment or kept under constant darkness for control dark treatment. The fish were anesthetized in 1.5mM Tricane Sigma and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light  and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle  corresponding to CT2  6  10  14  18 and 22. For mRNA seq  pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen. library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall  6 libraries 3 light groups and 3 dark groups were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics  Italy. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed. On average  6.7 million paired end reads were obtained for each library. The reads were of 2x100 base pairs.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,l1_pineal_ATCACG_L002_R2_001.fastq l1_pineal_ATCACG_L002_R1_001.fastq,fastq fastq,157696200.0,788481.0,Pineal gland light R1 run,0:101 1:99,A:41851978;C:36357694;G:36173225;T:41883697;N:1429606,101,99,,,41851978,36357694,36173225,41883697,1429606,SRX363281,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.84634,0.81043,0.11575,0.11592,0.73397,0.73829,0.48622,0.48559,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36569,SRR592709,SRX195414,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT10b,Pineal gland CT10b,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,12_zebrapg_CTTGTA_L001_R1.fastq,fastq,2267299914.0,11224257.0,Pineal gland CT10b run,0:101 1:101,A:607709328;C:525388699;G:526914662;T:602638305;N:4648920,101,101,,,607709328,525388699,526914662,602638305,4648920,SRX195414,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91476,0.91223,0.13127,0.13216,0.69061,0.69357,0.4519,0.45883,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36570,SRR592708,SRX195413,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT6b,Pineal gland CT6b,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,11_zebrapg_GGCTAC_L001_R1.fastq,fastq,1959732492.0,9701646.0,Pineal gland CT6b run,0:101 1:101,A:539256839;C:439457590;G:440064434;T:536966859;N:3986770,101,101,,,539256839,439457590,440064434,536966859,3986770,SRX195413,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90016,0.89453,0.15085,0.15152,0.68669,0.68972,0.46594,0.46791,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36571,SRR592707,SRX195412,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT2b,Pineal gland CT2b,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,2453741672.0,12147236.0,Pineal gland CT2b run,0:101 1:101,A:634387433;C:592849406;G:591345951;T:630233237;N:4925645,101,101,,,634387433,592849406,591345951,630233237,4925645,SRX195412,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90708,0.90474,0.16568,0.16764,0.70755,0.70914,0.49572,0.50509,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36572,SRR592705,SRX195411,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT18b,Pineal gland CT18b,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,2178785332.0,10786066.0,Pineal gland CT18b run,0:101 1:101,A:594834306;C:495808338;G:493409173;T:590321583;N:4411932,101,101,,,594834306,495808338,493409173,590321583,4411932,SRX195411,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89881,0.89552,0.13767,0.13768,0.69215,0.69542,0.45042,0.45067,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36573,SRR592703,SRX195410,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT10,Pineal gland CT10,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,6_zebrapg_GCCAAT_L001_R1.fastq,fastq,2264856522.0,11212161.0,Pineal gland CT10 run,0:101 1:101,A:618511903;C:514367008;G:514553380;T:612826453;N:4597778,101,101,,,618511903,514367008,514553380,612826453,4597778,SRX195410,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.9147,0.91201,0.14139,0.14232,0.66892,0.67225,0.46449,0.46385,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-12-14,Adult,Adult,Pineal Gland,Endocrine System
36574,SRR592702,SRX195409,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT6,Pineal gland CT6,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,4862235950.0,24070475.0,Pineal gland CT6 run,0:101 1:101,A:1301039088;C:1130011170;G:1129039062;T:1292258043;N:9888587,101,101,,,1301039088,1130011170,1129039062,1292258043,9888587,SRX195409,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91831,0.91455,0.12082,0.12144,0.6827,0.68625,0.46641,0.46572,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36575,SRR592701,SRX195408,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT2,Pineal gland CT2,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,2765620178.0,13691189.0,Pineal gland CT2 run,0:101 1:101,A:732432924;C:649046085;G:650686268;T:727912942;N:5541959,101,101,,,732432924,649046085,650686268,727912942,5541959,SRX195408,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91765,0.9136,0.10747,0.1072,0.67085,0.6733,0.46153,0.45978,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36576,SRR592700,SRX195407,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT22,Pineal gland CT22,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,1547066490.0,7658745.0,Pineal gland CT22 run,0:101 1:101,A:420761054;C:353199899;G:352761515;T:417226020;N:3118002,101,101,,,420761054,353199899,352761515,417226020,3118002,SRX195407,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89945,0.8894,0.13461,0.13453,0.67334,0.6772,0.47399,0.47311,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36577,SRR592706,SRX195406,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT22b,Pineal gland CT22b,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,1732363308.0,16983954.0,Pineal gland CT22b run,0:51 1:51,A:460560266;C:406133382;G:400603421;T:464930271;N:135968,51,51,,,460560266,406133382,400603421,464930271,135968,SRX195406,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89284,0.88902,0.1375,0.13615,0.68178,0.68138,0.46301,0.46538,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36578,SRR592704,SRX195405,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT14b,Pineal gland CT14b,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,7_zebr_pg_CAGATC_L007_R1.fastq,fastq,1395806454.0,13684377.0,Pineal gland CT14b run,0:51 1:51,A:372939800;C:324349097;G:332976129;T:365435447;N:105981,51,51,,,372939800,324349097,332976129,365435447,105981,SRX195405,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.87193,0.87656,0.13322,0.13509,0.70084,0.70289,0.45121,0.45269,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36579,SRR592699,SRX195404,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT18,Pineal gland CT18,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,1668838014.0,16361157.0,Pineal gland CT18 run,0:51 1:51,A:442604920;C:391602372;G:388058181;T:446247320;N:325221,51,51,,,442604920,391602372,388058181,446247320,325221,SRX195404,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89426,0.89144,0.13522,0.13581,0.68499,0.6859,0.46605,0.46445,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36580,SRR592698,SRX195403,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT14,Pineal gland CT14,1,library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly  starting from total RNA  the messenger RNA was purified using polyA selection  then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards  the second strand was generated to create double stranded cDNA. Finally  adapters were added by ligation to the double stranded cDNA  which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip  clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used  one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares  Illumina indexes separation was also performed.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,1_zebr_pg_ATCACG_L006_R1.fastq,fastq,1426289358.0,13983229.0,Pineal gland CT14 run,0:51 1:51,A:378980680;C:335425123;G:329692368;T:381915783;N:275404,51,51,,,378980680,335425123,329692368,381915783,275404,SRX195403,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.85247,0.85003,0.12173,0.12294,0.69694,0.69781,0.46706,0.46744,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-12-14,Adult,Adult,Pineal Gland,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. Overall design: Determination of gene expression levels in centroacinar cells and non centroacinar cells from adult pancreas.,,pubmed:26153247,,non CAC rep 2,GSM1875475,,source name:pancreas non CAC|tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated non centroacinar cells,non 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 non CAC,,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,,tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated non centroacinar cells,GSM1875475,GSM1875475: non CAC rep 2; Danio rerio; RNA Seq,GSM1875475,,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:GSM1875475,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP063624,,,H0J49ADXXs_2_2_merged.fastq.bz2,fastq,8206500750.0,109420010.0,GSM1875475 r1,0:75,A:2316013641;C:1680081024;G:1838151157;T:2362455717;N:9799211,75,,,,2316013641,1680081024,1838151157,2362455717,9799211,SRX1225282,SRS1065171,SRA297337,GEO,"Institute of Genetic Medicine, Johns Hopkins University",1,0.5785,,0.17732,,0.77469,,0.62483,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2015-09-11,Adult,Adult,Pancreas,Endocrine System
39918,SRR2353209,SRX1225281,SRS1065172,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.,,pubmed:26153247,,CAC rep 2,GSM1875474,,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,,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,,tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated centroacinar cells,GSM1875474,GSM1875474: CAC rep 2; Danio rerio; RNA Seq,GSM1875474,,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:GSM1875474,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP063624,,,H0J49ADXXs_2_1_merged.fastq.bz2,fastq,8206500750.0,109420010.0,GSM1875474 r1,0:75,A:2399854503;C:1714800726;G:1801618139;T:2289278152;N:949230,75,,,,2399854503,1714800726,1801618139,2289278152,949230,SRX1225281,SRS1065172,SRA297337,GEO,"Institute of Genetic Medicine, Johns Hopkins University",1,0.66738,,0.21282,,0.75694,,0.6409,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2015-09-11,Adult,Adult,Pancreas,Endocrine System
39919,SRR2353208,SRX1225280,SRS1065173,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.,,pubmed:26153247,,non CAC rep 1,GSM1875473,,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,,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,,tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated non centroacinar cells,GSM1875473,GSM1875473: non CAC rep 1; Danio rerio; RNA Seq,GSM1875473,,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,,SRP063624,,,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,,,,2352532315,1630885687,1811590860,2358426654,14473609,SRX1225280,SRS1065173,SRA297337,GEO,"Institute of Genetic Medicine, Johns Hopkins University",1,0.56456,,0.17736,,0.74525,,0.57983,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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.,,pubmed:26153247,,CAC rep 1,GSM1875472,,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,,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,,tissue:pancreas|developmental stage:adult|strain:AB|cell type:isolated centroacinar cells,GSM1875472,GSM1875472: CAC rep 1; Danio rerio; RNA Seq,GSM1875472,,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,,SRP063624,,,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,,,,2418955841,1674627530,1764871153,2308386909,1067692,SRX1225279,SRS1065174,SRA297337,GEO,"Institute of Genetic Medicine, Johns Hopkins University",1,0.66215,,0.21771,,0.72437,,0.57789,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2015-09-11,Adult,Adult,Pancreas,Endocrine System
42004,SRR5381358,SRX2676477,SRS2074974,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adulttom 3,GSM2551537,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM zebrafish,adulttom 3,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM zebrafish,GSM2551537,GSM2551537: adulttom 3; Danio rerio; RNA Seq,GSM2551537,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551537,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_TOM3.R1.fastq.gz Sample_TOM4.R2.fastq.gz,fastq fastq,1609605492.0,15780446.0,GSM2551537 r1,0:51 1:51,A:415499066;C:388312214;G:385728681;T:415857517;N:4208014,51,51,,,415499066,388312214,385728681,415857517,4208014,SRX2676477,SRS2074974,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.80564,0.81722,0.079,0.08136,0.70583,0.70615,0.47218,0.47209,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42005,SRR5381357,SRX2676476,SRS2074973,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adulttom 2,GSM2551536,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM zebrafish,adulttom 2,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM zebrafish,GSM2551536,GSM2551536: adulttom 2; Danio rerio; RNA Seq,GSM2551536,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551536,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_TOM2.R1.fastq.gz Sample_TOM2.R2.fastq.gz,fastq fastq,1935298122.0,18973511.0,GSM2551536 r1,0:51 1:51,A:508498437;C:457892392;G:456480020;T:507338327;N:5088946,51,51,,,508498437,457892392,456480020,507338327,5088946,SRX2676476,SRS2074973,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.83172,0.84227,0.08076,0.08245,0.7039,0.70333,0.4811,0.47791,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42006,SRR5381356,SRX2676475,SRS2074972,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adulttom 1,GSM2551535,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM zebrafish,adulttom 1,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM zebrafish,GSM2551535,GSM2551535: adulttom 1; Danio rerio; RNA Seq,GSM2551535,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551535,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_TOM1.R1.fastq.gz Sample_TOM1.R2.fastq.gz,fastq fastq,2052542532.0,20122966.0,GSM2551535 r1,0:51 1:51,A:538557760;C:487047846;G:480533246;T:541009818;N:5393862,51,51,,,538557760,487047846,480533246,541009818,5393862,SRX2676475,SRS2074972,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.83624,0.84747,0.08987,0.09268,0.69467,0.69305,0.49138,0.49386,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42007,SRR5381355,SRX2676474,SRS2074971,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adultbraf 5,GSM2551534,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,adultbraf 5,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,GSM2551534,GSM2551534: adultbraf 5; Danio rerio; RNA Seq,GSM2551534,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551534,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_BRAF5.R1.fastq.gz Sample_BRAF5.R2.fastq.gz,fastq fastq,1940919750.0,19028625.0,GSM2551534 r1,0:51 1:51,A:507148079;C:461510577;G:459738307;T:507437006;N:5085781,51,51,,,507148079,461510577,459738307,507437006,5085781,SRX2676474,SRS2074971,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.79926,0.81264,0.09051,0.09347,0.70339,0.70212,0.49811,0.5006,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42008,SRR5381354,SRX2676473,SRS2074970,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adultbraf 4,GSM2551533,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,adultbraf 4,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,GSM2551533,GSM2551533: adultbraf 4; Danio rerio; RNA Seq,GSM2551533,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551533,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_BRAF4.R1.fastq.gz Sample_BRAF4.R2.fastq.gz,fastq fastq,2015653926.0,19761313.0,GSM2551533 r1,0:51 1:51,A:530268431;C:476921090;G:472904433;T:530254613;N:5305359,51,51,,,530268431,476921090,472904433,530254613,5305359,SRX2676473,SRS2074970,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.82386,0.83094,0.08532,0.08667,0.69822,0.69842,0.48917,0.49445,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42009,SRR5381353,SRX2676472,SRS2074969,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adultbraf 3,GSM2551532,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,adultbraf 3,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,GSM2551532,GSM2551532: adultbraf 3; Danio rerio; RNA Seq,GSM2551532,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551532,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_BRAF3.R1.fastq.gz Sample_BRAF3.R2.fastq.gz,fastq fastq,1663763820.0,16311410.0,GSM2551532 r1,0:51 1:51,A:436209611;C:395497900;G:390361982;T:437328416;N:4365911,51,51,,,436209611,395497900,390361982,437328416,4365911,SRX2676472,SRS2074969,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.82532,0.83722,0.07867,0.08086,0.70232,0.70216,0.49285,0.48414,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42010,SRR5381352,SRX2676471,SRS2074968,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adultbraf 2,GSM2551531,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,adultbraf 2,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,GSM2551531,GSM2551531: adultbraf 2; Danio rerio; RNA Seq,GSM2551531,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551531,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_BRAF2.R1.fastq.gz Sample_BRAF2.R2.fastq.gz,fastq fastq,1637414772.0,16053086.0,GSM2551531 r1,0:51 1:51,A:428301405;C:389554255;G:386807826;T:428450327;N:4300959,51,51,,,428301405,389554255,386807826,428450327,4300959,SRX2676471,SRS2074968,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.8282,0.84287,0.08238,0.08441,0.70224,0.70128,0.48094,0.48399,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42011,SRR5381351,SRX2676470,SRS2074967,SRP102546,PRJNA380660,Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression,GSE97096,Transcriptome Analysis,Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.,,pubmed:28350298,,adultbraf 1,GSM2551530,,source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,adultbraf 1,Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70,transgenic adult fish,,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,,tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish,GSM2551530,GSM2551530: adultbraf 1; Danio rerio; RNA Seq,GSM2551530,,1,RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol,GEO Accession:GSM2551530,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102546,,,Sample_BRAF1.R1.fastq.gz Sample_BRAF1.R2.fastq.gz,fastq fastq,1645146984.0,16128892.0,GSM2551530 r1,0:51 1:51,A:433917351;C:388216392;G:384485747;T:434178837;N:4348657,51,51,,,433917351,388216392,384485747,434178837,4348657,SRX2676470,SRS2074967,SRA549625,GEO,"Surgery, Weill Cornell Medical College",2,0.79957,0.8129,0.08255,0.08587,0.70341,0.70301,0.47963,0.47656,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-27,Adult,Adult,Thyroid,Endocrine System
42457,SRR5599696,SRX2853245,SRS2224927,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Night,GSM2640447,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,Pineal Gland Night,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,GSM2640447,GSM2640447: Pineal Gland Night; Danio rerio; RNA Seq,GSM2640447,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640447,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_night_ACAGTG_L001_R2_001.fastq.gz pineal_night_ACAGTG_L001_R1_001.fastq.gz,fastq fastq,2524070600.0,12620353.0,GSM2640447 r1,0:100 1:100,A:741805672;C:522977974;G:524367955;T:733520495;N:1398504,100,100,,,741805672,522977974,524367955,733520495,1398504,SRX2853245,SRS2224927,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.8882,0.89515,0.19772,0.1879,0.7021,0.70558,0.48908,0.487,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
42458,SRR5599697,SRX2853245,SRS2224927,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Night,GSM2640447,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,Pineal Gland Night,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,GSM2640447,GSM2640447: Pineal Gland Night; Danio rerio; RNA Seq,GSM2640447,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640447,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_night_ACAGTG_L002_R1_001.fastq.gz pineal_night_ACAGTG_L002_R2_001.fastq.gz,fastq fastq,2481727800.0,12408639.0,GSM2640447 r2,0:100 1:100,A:729161022;C:514502873;G:515738117;T:720993212;N:1332576,100,100,,,729161022,514502873,515738117,720993212,1332576,SRX2853245,SRS2224927,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.88828,0.89524,0.19981,0.18859,0.70418,0.70613,0.48446,0.49385,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
42459,SRR5599694,SRX2853244,SRS2224926,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Day,GSM2640446,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,Pineal Gland Day,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,GSM2640446,GSM2640446: Pineal Gland Day; Danio rerio; RNA Seq,GSM2640446,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640446,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_day_TGACCA_L001_R1_001.fastq.gz pineal_day_TGACCA_L001_R2_001.fastq.gz,fastq fastq,2548229000.0,12741145.0,GSM2640446 r1,0:100 1:100,A:715059730;C:560972529;G:565884910;T:704927661;N:1384170,100,100,,,715059730,560972529,565884910,704927661,1384170,SRX2853244,SRS2224926,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.90563,0.91317,0.14689,0.1416,0.69682,0.70329,0.47374,0.47931,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
42460,SRR5599695,SRX2853244,SRS2224926,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Day,GSM2640446,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,Pineal Gland Day,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,GSM2640446,GSM2640446: Pineal Gland Day; Danio rerio; RNA Seq,GSM2640446,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma  and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands  whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640446,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_day_TGACCA_L002_R1_001.fastq.gz pineal_day_TGACCA_L002_R2_001.fastq.gz,fastq fastq,2505604600.0,12528023.0,GSM2640446 r2,0:100 1:100,A:703028440;C:551757119;G:556590046;T:692921366;N:1307629,100,100,,,703028440,551757119,556590046,692921366,1307629,SRX2853244,SRS2224926,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.90515,0.91255,0.14693,0.14214,0.69652,0.70313,0.47136,0.48018,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
44043,SRR6237746,SRX3345984,SRS2646512,SRP123109,PRJNA416462,Transcriptome of zebrafish neurohypophyseal astroglia pituicytes,GSE106371,Transcriptome Analysis,The hypothalamo neurohypophyseal system HNS is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections  endothelial blood vessels and astroglial like cells  termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro vascular interface  which allows the release of neurohormones from the brain to the periphery. However  the molecular blueprint of pituicytes specific genes is  still unknown.  We have labelled and isolated  zebrafish pituicytes cells and have  identified their  molecular signature. Overall design: mRNA profiles of hypophyseal b Ala Lys Ne positive pituicytes and b Ala Lys Ne negative non pituicytes were generated by next generation sequencing  in 5 biological replicates  using Illumina HiSeq 2500 v4 instrument,,pubmed:30449506,,Sample Plate2 A6 AMCA,GSM2836694,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,354923207,259144918,256606445,359057403,163849,SRX3345984,SRS2646512,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.87646,,0.26527,,0.8257,,0.55303,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate2 A5 AMCA,GSM2836693,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,282028510,179853567,179383383,284281435,129692,SRX3345983,SRS2646515,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.90747,,0.36422,,0.74215,,0.54419,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate2 A4 AMCA,GSM2836692,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,339245851,240318483,237965388,342331066,153541,SRX3345982,SRS2646511,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.89175,,0.24416,,0.82384,,0.55389,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate2 A3 AMCA,GSM2836691,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,257233140,169854422,169238352,259211059,118891,SRX3345981,SRS2646513,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.90605,,0.30761,,0.74067,,0.55271,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate2 A2 AMCA,GSM2836690,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,326281148,256738933,252744782,332989234,155374,SRX3345980,SRS2646514,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.88849,,0.1697,,0.86602,,0.52913,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate2 A1 AMCA,GSM2836689,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,271804923,184830364,184695096,273646193,129553,SRX3345979,SRS2646510,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.909,,0.28209,,0.74582,,0.54537,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate1 A8 AMCA,GSM2836688,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,346218731,240547553,237863913,349847274,158738,SRX3345978,SRS2646509,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.89653,,0.29731,,0.82388,,0.57688,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate1 A7 AMCA,GSM2836687,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,281188323,177657384,177254638,282775426,129174,SRX3345977,SRS2646507,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.8999,,0.31855,,0.7643,,0.56856,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate1 A6 AMCA,GSM2836686,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,366468588,242252329,239380324,369298417,167612,SRX3345976,SRS2646506,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.87327,,0.29592,,0.86026,,0.61414,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,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,,pubmed:30449506,,Sample Plate1 A5 AMCA,GSM2836685,,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 β 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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,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 250µL 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 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C 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 μm 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 70µm 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°C. 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® Ultra™ 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,,SRP123109,,,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,,,304872127,192446811,191928153,306392280,141949,SRX3345975,SRS2646508,SRA626615,GEO,"Bioinformatics Unit, Biological Services, Weizmann Institute of Science",1,0.90464,,0.36217,,0.74836,,0.56177,,61,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Israel,2017-10-31,Adult,Adult,Pituitary Gland,Endocrine System
44907,SRR6293905,SRX3395016,SRS2689202,SRP125042,PRJNA418467,Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish,GSE106938,Transcriptome Analysis,Individual organisms age at different rates  however  it remains unclear how aging alters the properties of individual cells.  Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age.  Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress  inhibition of growth factor signaling and inflammation  including NF kB signaling.  Using a reporter line  we show that NF kB signaling is indeed activated heterogeneously with age.  Notably  beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity.  Furthermore  NF kB signalinghigh beta cells from younger islets upregulate socs2  a gene naturally expressed in beta cells from older islets.  In turn  socs2 can inhibit proliferation cell autonomously.  NF kB activation correlates with the recruitment of tnfa expressing immune cells  pointing towards a role for the islet microenvironment in this activity.  We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome  GRCz10  using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.,,pubmed:29624168,,1ypf rep2,GSM2857832,,tissue:beta cells|age:1 year|strain:Tgins:BB1.0L,1ypf rep2,Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count,beta cells,,FACS llumina HiSeq2500 in 2x75bp paired end mode,,age:1 year|strain:Tgins:BB1.0L,GSM2857832,GSM2857832: 1ypf rep2; Danio rerio; RNA Seq,GSM2857832,,1,FACS llumina HiSeq2500 in 2x75bp paired end mode,GEO Accession:GSM2857832,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125042,,,L10760_Track-31237_R1.fastq.gz L10760_Track-31237_R2.fastq.gz,fastq fastq,5627077088.0,37020244.0,GSM2857832 r1,0:76 1:76,A:1481195914;C:1302350910;G:1313408578;T:1524234346;N:5887340,76,76,,,1481195914,1302350910,1313408578,1524234346,5887340,SRX3395016,SRS2689202,SRA631121,GEO,"Ninov Lab, CRTD",2,0.84288,0.84015,0.15135,0.15241,0.75089,0.75436,0.60917,0.60027,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2017-11-15,Adult,Adult,Pancreas,Endocrine System
44908,SRR6293904,SRX3395015,SRS2689200,SRP125042,PRJNA418467,Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish,GSE106938,Transcriptome Analysis,Individual organisms age at different rates  however  it remains unclear how aging alters the properties of individual cells.  Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age.  Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress  inhibition of growth factor signaling and inflammation  including NF kB signaling.  Using a reporter line  we show that NF kB signaling is indeed activated heterogeneously with age.  Notably  beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity.  Furthermore  NF kB signalinghigh beta cells from younger islets upregulate socs2  a gene naturally expressed in beta cells from older islets.  In turn  socs2 can inhibit proliferation cell autonomously.  NF kB activation correlates with the recruitment of tnfa expressing immune cells  pointing towards a role for the islet microenvironment in this activity.  We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome  GRCz10  using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.,,pubmed:29624168,,1ypf rep1,GSM2857831,,tissue:beta cells|age:1 year|strain:Tgins:BB1.0L,1ypf rep1,Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count,beta cells,,FACS llumina HiSeq2500 in 2x75bp paired end mode,,age:1 year|strain:Tgins:BB1.0L,GSM2857831,GSM2857831: 1ypf rep1; Danio rerio; RNA Seq,GSM2857831,,1,FACS llumina HiSeq2500 in 2x75bp paired end mode,GEO Accession:GSM2857831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125042,,,L10759_Track-31236_R1.fastq.gz L10759_Track-31236_R2.fastq.gz,fastq fastq,5128054856.0,33737203.0,GSM2857831 r1,0:76 1:76,A:1350542699;C:1184925079;G:1197353068;T:1389942509;N:5291501,76,76,,,1350542699,1184925079,1197353068,1389942509,5291501,SRX3395015,SRS2689200,SRA631121,GEO,"Ninov Lab, CRTD",2,0.84827,0.85287,0.16376,0.1636,0.75645,0.75797,0.59534,0.59534,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2017-11-15,Adult,Adult,Pancreas,Endocrine System
44909,SRR6293903,SRX3395014,SRS2689199,SRP125042,PRJNA418467,Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish,GSE106938,Transcriptome Analysis,Individual organisms age at different rates  however  it remains unclear how aging alters the properties of individual cells.  Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age.  Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress  inhibition of growth factor signaling and inflammation  including NF kB signaling.  Using a reporter line  we show that NF kB signaling is indeed activated heterogeneously with age.  Notably  beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity.  Furthermore  NF kB signalinghigh beta cells from younger islets upregulate socs2  a gene naturally expressed in beta cells from older islets.  In turn  socs2 can inhibit proliferation cell autonomously.  NF kB activation correlates with the recruitment of tnfa expressing immune cells  pointing towards a role for the islet microenvironment in this activity.  We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome  GRCz10  using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.,,pubmed:29624168,,3mpf rep1,GSM2857830,,tissue:beta cells|age:3 month|strain:Tgins:BB1.0L,3mpf rep1,Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count,beta cells,,FACS llumina HiSeq2500 in 2x75bp paired end mode,,age:3 month|strain:Tgins:BB1.0L,GSM2857830,GSM2857830: 3mpf rep1; Danio rerio; RNA Seq,GSM2857830,,1,FACS llumina HiSeq2500 in 2x75bp paired end mode,GEO Accession:GSM2857830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125042,,,L10758_Track-31235_R1.fastq.gz L10758_Track-31235_R2.fastq.gz,fastq fastq,4259609848.0,28023749.0,GSM2857830 r1,0:76 1:76,A:1095866394;C:1004201489;G:1014981602;T:1140141196;N:4419167,76,76,,,1095866394,1004201489,1014981602,1140141196,4419167,SRX3395014,SRS2689199,SRA631121,GEO,"Ninov Lab, CRTD",2,0.87618,0.87022,0.1249,0.12602,0.76368,0.76469,0.65739,0.64564,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2017-11-15,Adult,Adult,Pancreas,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.,,pubmed:30679186,,Il1B rep2,GSM3494234,,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,,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˚C 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˚C. 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,,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,,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˚C 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˚C. 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,,SRP171016,,,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,,,961171458,699797228,707162172,914140351,34423,SRX5073702,SRS4087528,SRA815642,GEO,"Ninov, CRTD",1,0.88789,,0.19663,,0.77461,,0.56289,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:30679186,,Il1B rep1,GSM3494233,,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,,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˚C 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˚C. 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,,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,,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˚C 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˚C. 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,,SRP171016,,,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,,,900337994,672684479,688186415,856137569,32031,SRX5073701,SRS4087527,SRA815642,GEO,"Ninov, CRTD",1,0.88054,,0.16457,,0.7735,,0.55887,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:30679186,,Con rep2,GSM3494232,,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,,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˚C 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˚C. 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,,genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type,GSM3494232,GSM3494232: Con rep2; Danio rerio; RNA Seq,GSM3494232,,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˚C 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˚C. 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,,SRP171016,,,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,,,,1137736314,843105511,852627922,1062822946,254819,SRX5073700,SRS4087526,SRA815642,GEO,"Ninov, CRTD",1,0.86977,,0.16515,,0.77078,,0.40368,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:30679186,,Con rep1,GSM3494231,,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,,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˚C 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˚C. 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,,genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type,GSM3494231,GSM3494231: Con rep1; Danio rerio; RNA Seq,GSM3494231,,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˚C 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˚C. 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,,SRP171016,,,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,,,,1081119100,816543927,821868656,1023236057,243052,SRX5073699,SRS4087525,SRA815642,GEO,"Ninov, CRTD",1,0.87612,,0.16984,,0.7684,,0.57882,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2018-11-28,Adult,Adult,Pancreas,Endocrine System
51051,SRR8456909,SRX5263565,SRS4264370,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,alms1MUT 2,GSM3569389,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,alms1MUT 2,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,GSM3569389,GSM3569389: alms1MUT 2; Danio rerio; RNA Seq,GSM3569389,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569389,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,alms1MUT-2_S204_R1_001.fastq.gz alms1MUT-2_S204_R2_001.fastq.gz,fastq fastq,34706891262.0,114923481.0,GSM3569389 r1,0:151 1:151,A:9976818172;C:7360068941;G:7101573916;T:10265591911;N:2838322,151,151,,,9976818172,7360068941,7101573916,10265591911,2838322,SRX5263565,SRS4264370,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.87723,0.87816,0.52783,0.53313,0.6729,0.69288,0.50497,0.5044,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System
51052,SRR8456908,SRX5263564,SRS4264369,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,alms1MUT 1,GSM3569388,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,alms1MUT 1,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,GSM3569388,GSM3569388: alms1MUT 1; Danio rerio; RNA Seq,GSM3569388,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569388,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,alms1MUT-1_S203_R1_001.fastq.gz alms1MUT-1_S203_R2_001.fastq.gz,fastq fastq,31132041158.0,103086229.0,GSM3569388 r1,0:151 1:151,A:8977930028;C:6567587111;G:6338188683;T:9245824930;N:2510406,151,151,,,8977930028,6567587111,6338188683,9245824930,2510406,SRX5263564,SRS4264369,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.87391,0.87469,0.49807,0.50313,0.68947,0.70449,0.51756,0.50827,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System
51053,SRR8456907,SRX5263563,SRS4264368,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,WT 2,GSM3569387,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,WT 2,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,GSM3569387,GSM3569387: WT 2; Danio rerio; RNA Seq,GSM3569387,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569387,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,WT-2_S202_R1_001.fastq.gz WT-2_S202_R2_001.fastq.gz,fastq fastq,33558516632.0,111120916.0,GSM3569387 r1,0:151 1:151,A:9387420547;C:7359835200;G:7201488528;T:9607046373;N:2725984,151,151,,,9387420547,7359835200,7201488528,9607046373,2725984,SRX5263563,SRS4264368,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.90113,0.9024,0.21941,0.22244,0.69572,0.70621,0.51483,0.51186,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System
51054,SRR8456906,SRX5263562,SRS4264367,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,WT 1,GSM3569386,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,WT 1,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,GSM3569386,GSM3569386: WT 1; Danio rerio; RNA Seq,GSM3569386,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al.  2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569386,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,WT-1_S201_R1_001.fastq.gz WT-1_S201_R2_001.fastq.gz,fastq fastq,35627069558.0,117970429.0,GSM3569386 r1,0:151 1:151,A:9789934413;C:8039430934;G:7849037733;T:9945758380;N:2908098,151,151,,,9789934413,8039430934,7849037733,9945758380,2908098,SRX5263562,SRS4264367,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.91881,0.91874,0.23468,0.24084,0.66616,0.67969,0.46826,0.46848,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System
55229,SRR10199493,SRX6919651,SRS5450537,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23PG replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:15 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,CHR23 PG1,CHR23 PG1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-PG1_combined_R1.fastq.gz Chr23-PG1_combined_R2.fastq.gz,fastq fastq,6654002100.0,22180007.0,Chr23 PG1 combined R1.fastq.gz,0:150 1:150,A:1819739632;C:1499478529;G:1515944103;T:1818620794;N:219042,150,150,,,1819739632,1499478529,1515944103,1818620794,219042,SRX6919651,SRS5450537,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92113,0.92255,0.09207,0.09331,0.71573,0.7205,0.52726,0.58205,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55241,SRR10199505,SRX6919639,SRS5450525,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTPG replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:20 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,WT PG3,WT PG3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-PG3_combined_R1.fastq.gz WT-PG3_combined_R2.fastq.gz,fastq fastq,6751713000.0,22505710.0,WT PG3 combined R1.fastq.gz,0:150 1:150,A:1869416559;C:1496572806;G:1514851553;T:1870652394;N:219688,150,150,,,1869416559,1496572806,1514851553,1870652394,219688,SRX6919639,SRS5450525,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92953,0.93151,0.09098,0.09156,0.73074,0.73699,0.66993,0.67339,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55242,SRR10199506,SRX6919638,SRS5450524,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTPG replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:19 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,WT PG2,WT PG2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-PG2_combined_R1.fastq.gz WT-PG2_combined_R2.fastq.gz,fastq fastq,6370809600.0,21236032.0,WT PG2 combined R1.fastq.gz,0:150 1:150,A:1787150048;C:1388750804;G:1405374191;T:1789322231;N:212326,150,150,,,1787150048,1388750804,1405374191,1789322231,212326,SRX6919638,SRS5450524,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.9274,0.92797,0.09768,0.09788,0.7288,0.73387,0.6714,0.67474,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55243,SRR10199507,SRX6919637,SRS5450523,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,WTPG replicate 1,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:18 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,WT PG1,WT PG1,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,WT-PG1_combined_R1.fastq.gz WT-PG1_combined_R2.fastq.gz,fastq fastq,7088374200.0,23627914.0,WT PG1 combined R1.fastq.gz,0:150 1:150,A:1976454953;C:1556957648;G:1576097593;T:1978627198;N:236808,150,150,,,1976454953,1556957648,1576097593,1978627198,236808,SRX6919637,SRS5450523,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92813,0.92862,0.09435,0.09468,0.73072,0.73732,0.67177,0.67649,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55244,SRR10199508,SRX6919636,SRS5450522,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23PG replicate 3,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:17 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,CHR23 PG3,CHR23 PG3,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-PG3_combined_R1.fastq.gz Chr23-PG3_combined_R2.fastq.gz,fastq fastq,6306831900.0,21022773.0,Chr23 PG3 combined R1.fastq.gz,0:150 1:150,A:1761625771;C:1384630771;G:1399189529;T:1761175818;N:210011,150,150,,,1761625771,1384630771,1399189529,1761175818,210011,SRX6919636,SRS5450522,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.91822,0.91897,0.09779,0.09773,0.71676,0.72198,0.59874,0.52969,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,Endocrine System
55245,SRR10199509,SRX6919635,SRS5450521,SRP223604,PRJNA574807,comparative transcriptome between wildtype and chr23 KO zebrafish.,PRJNA574807,Other,the comparative transcriptome between wildtype and chr23 KO zebrafish were analyzed to uncover the cause of the failure of the oocyte maturation and ovulation in chr23 KO.,,,,,Chr23PG replicate 2,,strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:16 month|dev stage:sex mature|sex:female|tissue:pituitaty|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female  pituitary,CHR23 PG2,CHR23 PG2,the libraries were constructed and sequenced on Illumina HiSeq using paired end protocol by GENEWIZ Biotechnology Co.  LTD,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,HiSeq X Ten,,SRP223604,,,Chr23-PG2_combined_R1.fastq.gz Chr23-PG2_combined_R2.fastq.gz,fastq fastq,6790899600.0,22636332.0,Chr23 PG2 combined R1.fastq.gz,0:150 1:150,A:1842525837;C:1545697169;G:1560457672;T:1841998398;N:220524,150,150,,,1842525837,1545697169,1560457672,1841998398,220524,SRX6919635,SRS5450521,SRA969652,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92407,0.92584,0.0916,0.09113,0.71644,0.72141,0.5239,0.59097,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-29,Adult,Adult,Pituitary Gland,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.,,,,Pancreas islets   Pancreas islet 6dpf B2,Pancreas islets   Islet 6d B2 AGN000787,,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,,,,,,,,,Pancreas islets   Pancreas islet 6dpf B2,AGR001074,AGR001074,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,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,,,144866246,90980862,90828673,140671264,21035,SRX10633820,SRS8730202,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.86223,,0.47625,,0.68556,,0.52132,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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.,,,,Pancreas islets   Pancreas islet 6dpf B1,Pancreas islets   Islet 6d B1 AGN000786,,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,,,,,,,,,Pancreas islets   Pancreas islet 6dpf B1,AGR001073,AGR001073,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,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,,,179281934,120318002,119990438,172891644,24774,SRX10633819,SRS8730201,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.84252,,0.35277,,0.69219,,0.54723,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2,Pancreas islets   Islet SST b cell abt 4d B2 AGN000782,,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,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2,AGR001070,AGR001070,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,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,,,151409804,91026556,90673968,148189727,20561,SRX10633814,SRS8730196,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.82954,,0.59765,,0.75538,,0.53049,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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. Overall  our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1,Pancreas islets   Islet SST b cell abt 4d B1 AGN000781,,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:AGN000781|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1,AGR001069,AGR001069,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001069_R1.fastq.gz,fastq,379230956.0,4989881.0,AGR001069 R1.fastq.gz,0:76 1:0,A:116227158;C:75587948;G:75371178;T:112027929;N:16743,76,0,,,116227158,75587948,75371178,112027929,16743,SRX10633813,SRS8730195,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.87385,,0.38949,,0.69242,,0.47061,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64133,SRR14272179,SRX10633809,SRS8730192,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.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B2,Pancreas islets   Islet SST 4d B2 AGN000780,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000678|replicate ref:AGN000780|replicate order:2|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B2,AGR001068,AGR001068,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001068_R1.fastq.gz,fastq,1025641204.0,13495279.0,AGR001068 R1.fastq.gz,0:76 1:0,A:313399325;C:201992871;G:202026959;T:308179140;N:42909,76,0,,,313399325,201992871,202026959,308179140,42909,SRX10633809,SRS8730192,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.8692,,0.47406,,0.68081,,0.54006,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
64134,SRR14272180,SRX10633808,SRS8730191,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.,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B1,Pancreas islets   Islet SST 4d B1 AGN000779,,strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000678|replicate ref:AGN000779|replicate order:1|BioSampleModel:Model organism or animal,,,,,,,,,Pancreas islets   Pancreas islet 4dpf somatostatin transgene sst2:RFP B1,AGR001067,AGR001067,mRNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP315319,,,AGR001067_R1.fastq.gz,fastq,645391392.0,8491992.0,AGR001067 R1.fastq.gz,0:76 1:0,A:198297729;C:127050955;G:126777924;T:193238145;N:26639,76,0,,,198297729,127050955,126777924,193238145,26639,SRX10633808,SRS8730191,SRA1220217,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.85746,,0.50636,,0.68286,,0.48271,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-04-19,Larval,Larval,Pancreas,Endocrine System
71089,SRR21237242,SRX17246664,SRS14811789,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration  we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,MTZ2,GSM6509761,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,MTZ2,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using  STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,GSM6509761,GSM6509761: MTZ2; Danio rerio; RNA Seq,GSM6509761 r1,GSM6509761,1,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_5_TAAGGCGA_L008_R2_001.fastq.gz IM_5_TAAGGCGA_L008_R1_001.fastq.gz,fastq fastq,15325310144.0,75867872.0,GSM6509761 r1,0:101 1:101,A:4269635088;C:3380943498;G:3260211685;T:4413526478;N:993395,101,101,,,4269635088,3380943498,3260211685,4413526478,993395,SRX17246664,SRS14811789,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.88443,0.88447,0.11507,0.11596,0.76686,0.7683,0.54694,0.55044,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System
71090,SRR21237243,SRX17246663,SRS14811788,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration  we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,MTZ3,GSM6509762,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,MTZ3,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using  STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,GSM6509762,GSM6509762: MTZ3; Danio rerio; RNA Seq,GSM6509762 r1,GSM6509762,1,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_6_CGTACTAG_L008_R2_001.fastq.gz IM_6_CGTACTAG_L008_R1_001.fastq.gz,fastq fastq,19255819276.0,95325838.0,GSM6509762 r1,0:101 1:101,A:5280171088;C:4359058370;G:4172558504;T:5442855832;N:1175482,101,101,,,5280171088,4359058370,4172558504,5442855832,1175482,SRX17246663,SRS14811788,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.90632,0.90614,0.08652,0.08772,0.76534,0.76696,0.52454,0.52158,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System
71091,SRR21237244,SRX17246662,SRS14811787,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration  we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,MTZ1,GSM6509760,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,MTZ1,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using  STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,GSM6509760,GSM6509760: MTZ1; Danio rerio; RNA Seq,GSM6509760 r1,GSM6509760,1,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_2_CGTACTAG_L006_R1_001.fastq.gz IM_2_CGTACTAG_L006_R2_001.fastq.gz,fastq fastq,17015359304.0,84234452.0,GSM6509760 r1,0:101 1:101,A:4643492769;C:3861165659;G:3730150815;T:4779151147;N:1398914,101,101,,,4643492769,3861165659,3730150815,4779151147,1398914,SRX17246662,SRS14811787,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.90217,0.90221,0.08047,0.08087,0.7651,0.76696,0.52075,0.53178,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System
71092,SRR21237245,SRX17246661,SRS14811786,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration  we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,Ductal3,GSM6509759,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,Ductal3,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using  STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,GSM6509759,GSM6509759: Ductal3; Danio rerio; RNA Seq,GSM6509759 r1,GSM6509759,1,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_4_CGTACTAG_L007_R2_001.fastq.gz IM_4_CGTACTAG_L007_R1_001.fastq.gz,fastq fastq,17851670816.0,88374608.0,GSM6509759 r1,0:101 1:101,A:5161409723;C:3739347454;G:3476991371;T:5472775357;N:1146911,101,101,,,5161409723,3739347454,3476991371,5472775357,1146911,SRX17246661,SRS14811786,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.85539,0.85497,0.14301,0.14391,0.78825,0.79115,0.52575,0.53365,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System
71093,SRR21237246,SRX17246660,SRS14811785,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration  we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,Ductal2,GSM6509758,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,Ductal2,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using  STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,GSM6509758,GSM6509758: Ductal2; Danio rerio; RNA Seq,GSM6509758 r1,GSM6509758,1,Lysis buffer : pure nuclease free water  triton 0 28%  dNTP 2 38mM   oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_3_TAAGGCGA_L007_R1_001.fastq.gz IM_3_TAAGGCGA_L007_R2_001.fastq.gz,fastq fastq,19081820314.0,94464457.0,GSM6509758 r1,0:101 1:101,A:5371144134;C:4166520026;G:3947780866;T:5595082921;N:1292367,101,101,,,5371144134,4166520026,3947780866,5595082921,1292367,SRX17246660,SRS14811785,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.88865,0.88865,0.14515,0.14711,0.7768,0.77857,0.53802,0.54651,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System