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1,453 rows where devstage_curation = "Adult" and tissue_curation_coarse = "Endocrine System"

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tissue_curation 4

technology 4

experiment.library_selection 4

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Endocrine System · 1,453 ✖

experiment.platform 1

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 1,453 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
321 321 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
330 330 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
331 331 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
332 332 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
333 333 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
334 334 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 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 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 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 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 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 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
33294 33294 SRR29920543 SRX25414719 SRS22075127 SRP521426 PRJNA1138768 Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics GSE272806 Transcriptome Analysis Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish however is an exception as gnrh3–/– fish which lack the hypophysiotropic GnRH3 are fertile suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2 thyroid hormone estrogen dopamine and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes instead the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2 but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression probably via a non Gnrh receptor route. Altogether while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing   pubmed:39499852   gnrh3 knockout scRNAseq GSM8412848   source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female|geo loc name:missing|collection date:missing gnrh3 knockout scRNAseq Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control normalization data integration and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files matrix file and comma separated values file Pituitary   Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample.   tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female GSM8412848 GSM8412848: gnrh3 knockout scRNAseq; Danio rerio; RNA Seq GSM8412848 r1 GSM8412848 1 Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP521426   loader:fastq load.py KO_20210616_A00904_IL100185604_S1_L001_I1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_I2_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 27063230346.0 121906443.0 GSM8412848 r1 0:10 1:10 2:101 3:101 A:6434793761;C:4051189285;G:4401327014;T:9737249538;N:541888 10 10 101 101 6434793761 4051189285 4401327014 9737249538 541888 SRX25414719 SRS22075127 SRA1930291 Stanford University Stanford University 2 0.10559 0.92046 0.02334 0.15386 0.97879 0.81732 0.68611 0.62975 101 101 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-07-22 Adult Adult Pituitary Gland Endocrine System
33295 33295 SRR29920544 SRX25414718 SRS22075126 SRP521426 PRJNA1138768 Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics GSE272806 Transcriptome Analysis Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish however is an exception as gnrh3–/– fish which lack the hypophysiotropic GnRH3 are fertile suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2 thyroid hormone estrogen dopamine and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes instead the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2 but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression probably via a non Gnrh receptor route. Altogether while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing   pubmed:39499852   WT scRNAseq GSM8412847   source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:wild type|Sex:female|geo loc name:missing|collection date:missing WT scRNAseq Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control normalization data integration and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files matrix file and comma separated values file Pituitary   Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample.   tissue:Pituitary|age:Adult 3 mpf|genotype:wild type|Sex:female GSM8412847 GSM8412847: WT scRNAseq; Danio rerio; RNA Seq GSM8412847 r1 GSM8412847 1 Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes with gently pipetting every 10 minutes using a wide bore tip. post incubation the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded then 1 mL Accumax working solution 30% Accumax in PBS was added and the cells were gently resuspended. post incubation at room temperature for 5 minutes the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C the supernatant was removed and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP521426   loader:fastq load.py WT_20210616_A00904_IL100185603_S1_L001_I1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_I2_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 26784946020.0 120652910.0 GSM8412847 r1 0:10 1:10 2:101 3:101 A:6396247260;C:3989076165;G:4295547390;T:9690479627;N:537378 10 10 101 101 6396247260 3989076165 4295547390 9690479627 537378 SRX25414718 SRS22075126 SRA1930291 Stanford University Stanford University 2 0.10896 0.92399 0.02311 0.16455 0.97652 0.80377 0.67721 0.64804 101 101 T B mate1 technical by mapping diff illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-07-22 Adult Adult Pituitary Gland Endocrine System
33348 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 …     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 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 …     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 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 …     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 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 …     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 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 …     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 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 …     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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ov…       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 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 ov…       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 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 ov…       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 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 ov…       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
43988 43988 SRR6811827 SRX3768867 SRS3023384 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 3 endo scar GSM3032170   source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult Pancreas 3 endo scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Primary pancreatic islet   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult GSM3032170 GSM3032170: Pancreas 3 endo scar; Danio rerio; OTHER GSM3032170   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032170 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     P7endo_scar_R1.fastq.gz P7endo_scar_R2.fastq.gz fastq fastq 2537781396.0 20465979.0 GSM3032170 r1 0:26 1:98 A:741745261;C:801599713;G:561531527;T:431666561;N:1238334 26 98     741745261 801599713 561531527 431666561 1238334 SRX3768867 SRS3023384 SRA623333 GEO Max Delbrück Center 2 0.00014 0.00289 0.00012 0.00028 0.99995 0.99602 1.0 0.68478 26 98 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Pancreas Endocrine System
43994 43994 SRR6811821 SRX3768861 SRS3023378 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Pancreas 3 endo mRNA GSM3032164   source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult Pancreas 3 endo mRNA Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes. Primary pancreatic islet   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult GSM3032164 GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq GSM3032164   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032164 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP121343     P7endo_wt_R1.fastq.gz P7endo_wt_R2.fastq.gz fastq fastq 41593781900.0 335433725.0 GSM3032164 r1 0:26 1:98 A:11833690021;C:9547054378;G:9724089290;T:10470148302;N:18799909 26 98     11833690021 9547054378 9724089290 10470148302 18799909 SRX3768861 SRS3023378 SRA623333 GEO Max Delbrück Center 2 0.00308 0.92936 0.00192 0.05695 0.9973 0.8686 0.45945 0.58814 26 98 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2018-03-06 Adult Adult Pancreas Endocrine System
44043 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 multip… 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 multip… 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 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 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 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
46259 46259 SRR7662165 SRX4522789 SRS3641107 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 40 GSM3325411   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 40 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325411 GSM3325411: 4mpf 3TD 40; Danio rerio; RNA Seq GSM3325411   1 FACS SMART Seq v4 GEO Accession:GSM3325411 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_40.fastq.gz fastq 46013820.0 605445.0 GSM3325411 r1 0:76 1:0 A:12185751;C:10519473;G:10377588;T:12930202;N:806 76 0     12185751 10519473 10377588 12930202 806 SRX4522789 SRS3641107 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.79173   0.06232   0.94728   0.70692   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46260 46260 SRR7662164 SRX4522788 SRS3641104 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 39 GSM3325410   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 39 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325410 GSM3325410: 4mpf 3TD 39; Danio rerio; RNA Seq GSM3325410   1 FACS SMART Seq v4 GEO Accession:GSM3325410 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_39.fastq.gz fastq 43118448.0 567348.0 GSM3325410 r1 0:76 1:0 A:11415668;C:9846910;G:9721395;T:12133691;N:784 76 0     11415668 9846910 9721395 12133691 784 SRX4522788 SRS3641104 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.81063   0.07048   0.94513   0.71805   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46261 46261 SRR7662163 SRX4522787 SRS3641101 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 38 GSM3325409   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 38 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325409 GSM3325409: 4mpf 3TD 38; Danio rerio; RNA Seq GSM3325409   1 FACS SMART Seq v4 GEO Accession:GSM3325409 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_38.fastq.gz fastq 44153644.0 580969.0 GSM3325409 r1 0:76 1:0 A:11395441;C:10637328;G:10522594;T:11597490;N:791 76 0     11395441 10637328 10522594 11597490 791 SRX4522787 SRS3641101 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.84207   0.05155   0.9567   0.59382   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46262 46262 SRR7662162 SRX4522786 SRS3641103 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 37 GSM3325408   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 37 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325408 GSM3325408: 4mpf 3TD 37; Danio rerio; RNA Seq GSM3325408   1 FACS SMART Seq v4 GEO Accession:GSM3325408 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_37.fastq.gz fastq 45082288.0 593188.0 GSM3325408 r1 0:76 1:0 A:11656775;C:10621119;G:10456207;T:12347402;N:785 76 0     11656775 10621119 10456207 12347402 785 SRX4522786 SRS3641103 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.81529   0.06896   0.94828   0.7399   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46263 46263 SRR7662161 SRX4522785 SRS3641100 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 36 GSM3325407   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 36 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325407 GSM3325407: 4mpf 3TD 36; Danio rerio; RNA Seq GSM3325407   1 FACS SMART Seq v4 GEO Accession:GSM3325407 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_36.fastq.gz fastq 43851468.0 576993.0 GSM3325407 r1 0:76 1:0 A:11646235;C:9975569;G:9837875;T:12391004;N:785 76 0     11646235 9975569 9837875 12391004 785 SRX4522785 SRS3641100 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.81855   0.10417   0.94653   0.705   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46264 46264 SRR7662160 SRX4522784 SRS3641102 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 35 GSM3325406   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 35 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325406 GSM3325406: 4mpf 3TD 35; Danio rerio; RNA Seq GSM3325406   1 FACS SMART Seq v4 GEO Accession:GSM3325406 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_35.fastq.gz fastq 51333820.0 675445.0 GSM3325406 r1 0:76 1:0 A:13522158;C:11828514;G:11668956;T:14313258;N:934 76 0     13522158 11828514 11668956 14313258 934 SRX4522784 SRS3641102 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.79211   0.07922   0.93361   0.67836   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46265 46265 SRR7662159 SRX4522783 SRS3641099 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 34 GSM3325405   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 34 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325405 GSM3325405: 4mpf 3TD 34; Danio rerio; RNA Seq GSM3325405   1 FACS SMART Seq v4 GEO Accession:GSM3325405 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_34.fastq.gz fastq 42434448.0 558348.0 GSM3325405 r1 0:76 1:0 A:11034253;C:9951444;G:9757025;T:11690994;N:732 76 0     11034253 9951444 9757025 11690994 732 SRX4522783 SRS3641099 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.80526   0.0836   0.94397   0.75354   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46266 46266 SRR7662158 SRX4522782 SRS3641097 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 33 GSM3325404   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 33 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325404 GSM3325404: 4mpf 3TD 33; Danio rerio; RNA Seq GSM3325404   1 FACS SMART Seq v4 GEO Accession:GSM3325404 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_33.fastq.gz fastq 41483080.0 545830.0 GSM3325404 r1 0:76 1:0 A:10943748;C:9539565;G:9367638;T:11631347;N:782 76 0     10943748 9539565 9367638 11631347 782 SRX4522782 SRS3641097 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.84811   0.0724   0.94079   0.70412   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46267 46267 SRR7662157 SRX4522781 SRS3641096 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 32 GSM3325403   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 32 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325403 GSM3325403: 4mpf 3TD 32; Danio rerio; RNA Seq GSM3325403   1 FACS SMART Seq v4 GEO Accession:GSM3325403 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_32.fastq.gz fastq 46634892.0 613617.0 GSM3325403 r1 0:76 1:0 A:12285344;C:10732177;G:10567037;T:13049373;N:961 76 0     12285344 10732177 10567037 13049373 961 SRX4522781 SRS3641096 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.7942   0.0631   0.94024   0.69769   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46268 46268 SRR7662156 SRX4522780 SRS3641098 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 31 GSM3325402   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 31 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325402 GSM3325402: 4mpf 3TD 31; Danio rerio; RNA Seq GSM3325402   1 FACS SMART Seq v4 GEO Accession:GSM3325402 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_31.fastq.gz fastq 38137864.0 501814.0 GSM3325402 r1 0:76 1:0 A:11280508;C:7576592;G:7684905;T:11595131;N:728 76 0     11280508 7576592 7684905 11595131 728 SRX4522780 SRS3641098 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.75454   0.31244   0.96404   0.83206   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46269 46269 SRR7662155 SRX4522779 SRS3641095 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 30 GSM3325401   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 30 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325401 GSM3325401: 4mpf 3TD 30; Danio rerio; RNA Seq GSM3325401   1 FACS SMART Seq v4 GEO Accession:GSM3325401 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_30.fastq.gz fastq 49097976.0 646026.0 GSM3325401 r1 0:76 1:0 A:12742428;C:11505538;G:11340150;T:13508959;N:901 76 0     12742428 11505538 11340150 13508959 901 SRX4522779 SRS3641095 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.81308   0.07957   0.94584   0.74123   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46270 46270 SRR7662154 SRX4522778 SRS3641094 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 29 GSM3325400   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 29 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325400 GSM3325400: 4mpf 3TD 29; Danio rerio; RNA Seq GSM3325400   1 FACS SMART Seq v4 GEO Accession:GSM3325400 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_29.fastq.gz fastq 45125152.0 593752.0 GSM3325400 r1 0:76 1:0 A:11801780;C:10486963;G:10345497;T:12489940;N:972 76 0     11801780 10486963 10345497 12489940 972 SRX4522778 SRS3641094 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.839   0.07636   0.94148   0.7489   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46271 46271 SRR7662153 SRX4522777 SRS3641090 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 28 GSM3325399   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 28 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325399 GSM3325399: 4mpf 3TD 28; Danio rerio; RNA Seq GSM3325399   1 FACS SMART Seq v4 GEO Accession:GSM3325399 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_28.fastq.gz fastq 44665808.0 587708.0 GSM3325399 r1 0:76 1:0 A:11700132;C:10404707;G:10277473;T:12282706;N:790 76 0     11700132 10404707 10277473 12282706 790 SRX4522777 SRS3641090 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.82673   0.09831   0.94673   0.70054   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46272 46272 SRR7662152 SRX4522776 SRS3641091 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 27 GSM3325398   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 27 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325398 GSM3325398: 4mpf 3TD 27; Danio rerio; RNA Seq GSM3325398   1 FACS SMART Seq v4 GEO Accession:GSM3325398 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_27.fastq.gz fastq 36148944.0 475644.0 GSM3325398 r1 0:76 1:0 A:9254193;C:8695996;G:8545834;T:9652334;N:587 76 0     9254193 8695996 8545834 9652334 587 SRX4522776 SRS3641091 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.84555   0.06314   0.95187   0.74348   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46273 46273 SRR7662151 SRX4522775 SRS3641092 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 26 GSM3325397   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 26 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325397 GSM3325397: 4mpf 3TD 26; Danio rerio; RNA Seq GSM3325397   1 FACS SMART Seq v4 GEO Accession:GSM3325397 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_26.fastq.gz fastq 39483976.0 519526.0 GSM3325397 r1 0:76 1:0 A:10243731;C:9320393;G:9145297;T:10773771;N:784 76 0     10243731 9320393 9145297 10773771 784 SRX4522775 SRS3641092 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.81192   0.0737   0.94509   0.73844   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46274 46274 SRR7662150 SRX4522774 SRS3641089 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 25 GSM3325396   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 25 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325396 GSM3325396: 4mpf 3TD 25; Danio rerio; RNA Seq GSM3325396   1 FACS SMART Seq v4 GEO Accession:GSM3325396 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_25.fastq.gz fastq 39361312.0 517912.0 GSM3325396 r1 0:76 1:0 A:10042879;C:9519207;G:9312521;T:10485999;N:706 76 0     10042879 9519207 9312521 10485999 706 SRX4522774 SRS3641089 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.8252   0.04127   0.94901   0.75046   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46275 46275 SRR7662149 SRX4522773 SRS3641088 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 24 GSM3325395   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 24 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325395 GSM3325395: 4mpf 3TD 24; Danio rerio; RNA Seq GSM3325395   1 FACS SMART Seq v4 GEO Accession:GSM3325395 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_24.fastq.gz fastq 47431676.0 624101.0 GSM3325395 r1 0:76 1:0 A:12495357;C:10870593;G:10708467;T:13356444;N:815 76 0     12495357 10870593 10708467 13356444 815 SRX4522773 SRS3641088 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.83398   0.07885   0.93608   0.72127   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46276 46276 SRR7662148 SRX4522772 SRS3641087 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 23 GSM3325394   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 23 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325394 GSM3325394: 4mpf 3TD 23; Danio rerio; RNA Seq GSM3325394   1 FACS SMART Seq v4 GEO Accession:GSM3325394 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_23.fastq.gz fastq 27242048.0 358448.0 GSM3325394 r1 0:76 1:0 A:8135321;C:5430241;G:5413461;T:8262532;N:493 76 0     8135321 5430241 5413461 8262532 493 SRX4522772 SRS3641087 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.7264   0.06277   0.99277   0.96356   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46277 46277 SRR7662147 SRX4522771 SRS3641086 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 22 GSM3325393   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 22 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325393 GSM3325393: 4mpf 3TD 22; Danio rerio; RNA Seq GSM3325393   1 FACS SMART Seq v4 GEO Accession:GSM3325393 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_22.fastq.gz fastq 47999320.0 631570.0 GSM3325393 r1 0:76 1:0 A:12468506;C:11445141;G:11330644;T:12754052;N:977 76 0     12468506 11445141 11330644 12754052 977 SRX4522771 SRS3641086 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.85839   0.0787   0.91648   0.72247   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46278 46278 SRR7662146 SRX4522770 SRS3641085 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 21 GSM3325392   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 21 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325392 GSM3325392: 4mpf 3TD 21; Danio rerio; RNA Seq GSM3325392   1 FACS SMART Seq v4 GEO Accession:GSM3325392 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_21.fastq.gz fastq 43447224.0 571674.0 GSM3325392 r1 0:76 1:0 A:11289500;C:10397979;G:10217101;T:11541647;N:997 76 0     11289500 10397979 10217101 11541647 997 SRX4522770 SRS3641085 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.85251   0.09879   0.95434   0.57235   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System
46279 46279 SRR7662145 SRX4522769 SRS3641083 SRP131808 PRJNA432257 Single cell RNA sequencing of zebrafish beta cells from various stages GSE109881 Transcriptome Analysis Age associated deterioration of cellular physiology leads to pathological conditions and detection of premature aging could provide a window for preventive therapies against age related diseases. For this methods that accurately evaluate cellular age are required. However such techniques are currently limited and based on post hoc evaluation using a limited set of histological markers. Development of a technique capable of predicting cellular age and its modifiers requires a framework that can robustly handle the noise associated with single cell sampling protocols. Here we implement GERAS GEnetic Reference for Age of Single cell a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displayed greater than 90% accuracy in predicting the chronological stage of zebrafish beta cells and human pancreatic cells. The framework demonstrates robustness against biological and technical noise as evaluated by its performance on independent samplings of single cells. Additionally GERAS enabled the evaluation of differences in calorie intake and body mass index on the aging of zebrafish and human cells respectively. We further harnessed the predictive power of GERAS to identify genome wide molecular factors that correlate with aging. We show that one of these factors junb which declines in expression with aging is necessary to maintain the proliferative state of juvenile beta cells. Our results showcase the applicability of a machine learning framework to predict the chronological stage of heterogeneous cell populations. The study demonstrates the utility of stage classifiers in assessing pro aging factors and uncovering candidate genes associated with premature aging. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from various stages. Cells were sorted into a 96 well plates and single cell library prepared using SMART Seq v4 Ultra Low Input RNA Kit …   pubmed:30464314   4mpf 3TD 20 GSM3325391   tissue:beta cells|age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding 4mpf 3TD 20 Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters Genome build: Zebrafish GRCz10 beta cells   FACS SMART Seq v4   age:4mpf|strain:Tgins:BB1.0L|feeding:3 times a day feeding GSM3325391 GSM3325391: 4mpf 3TD 20; Danio rerio; RNA Seq GSM3325391   1 FACS SMART Seq v4 GEO Accession:GSM3325391 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP131808     4mpf_3TD_20.fastq.gz fastq 39193352.0 515702.0 GSM3325391 r1 0:76 1:0 A:10220606;C:9138362;G:8983737;T:10849932;N:715 76 0     10220606 9138362 8983737 10849932 715 SRX4522769 SRS3641083 SRA654064 GEO Ninov Lab, Center for Regenerative Therapies Dresden 1 0.82235   0.0909   0.93661   0.74939   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Germany 2018-08-08 Adult Adult Pancreas Endocrine System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;