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39 rows where technology = "unknown", tissue_curation = "Pancreas" and tissue_curation_coarse = "Endocrine System"

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experiment.library_selection 3

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Endocrine System · 39 ✖

tissue_curation 1

  • Pancreas · 39 ✖

technology 1

  • unknown · 39 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

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
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
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
50713 50713 SRR8255922 SRX5073702 SRS4087528 SRP171016 PRJNA507363 Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection GSE123036 Transcriptome Analysis To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.   pubmed:30679186   Il1B rep2 GSM3494234   source name:Pancreatic beta cells|genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells Il1B rep2 Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Pancreatic beta cells   Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells GSM3494234 GSM3494234: Il1B rep2; Danio rerio; RNA Seq GSM3494234   1 Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3494234 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP171016     L19371_Track-47496_R1.fastq.gz fastq 3282305632.0 43188232.0 GSM3494234 r1 0:76 1:0 A:961171458;C:699797228;G:707162172;T:914140351;N:34423 76 0     961171458 699797228 707162172 914140351 34423 SRX5073702 SRS4087528 SRA815642 GEO Ninov, CRTD 1 0.88789   0.19663   0.77461   0.56289   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2018-11-28 Adult Adult Pancreas Endocrine System
50714 50714 SRR8255921 SRX5073701 SRS4087527 SRP171016 PRJNA507363 Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection GSE123036 Transcriptome Analysis To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.   pubmed:30679186   Il1B rep1 GSM3494233   source name:Pancreatic beta cells|genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells Il1B rep1 Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Pancreatic beta cells   Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:Tgins:IL1B; Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:Interleukin 1B expression in beta cells GSM3494233 GSM3494233: Il1B rep1; Danio rerio; RNA Seq GSM3494233   1 Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3494233 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP171016     L19370_Track-47495_R1.fastq.gz fastq 3117378488.0 41018138.0 GSM3494233 r1 0:76 1:0 A:900337994;C:672684479;G:688186415;T:856137569;N:32031 76 0     900337994 672684479 688186415 856137569 32031 SRX5073701 SRS4087527 SRA815642 GEO Ninov, CRTD 1 0.88054   0.16457   0.7735   0.55887   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2018-11-28 Adult Adult Pancreas Endocrine System
50715 50715 SRR8255920 SRX5073700 SRS4087526 SRP171016 PRJNA507363 Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection GSE123036 Transcriptome Analysis To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.   pubmed:30679186   Con rep2 GSM3494232   source name:Pancreatic beta cells|genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type Con rep2 Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Pancreatic beta cells   Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type GSM3494232 GSM3494232: Con rep2; Danio rerio; RNA Seq GSM3494232   1 Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3494232 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP171016     L19373_Track-47629_R1.fastq.gz fastq 3896547512.0 51270362.0 GSM3494232 r1 0:76 A:1137736314;C:843105511;G:852627922;T:1062822946;N:254819 76       1137736314 843105511 852627922 1062822946 254819 SRX5073700 SRS4087526 SRA815642 GEO Ninov, CRTD 1 0.86977   0.16515   0.77078   0.40368   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2018-11-28 Adult Adult Pancreas Endocrine System
50716 50716 SRR8255919 SRX5073699 SRS4087525 SRP171016 PRJNA507363 Modelling pancreatic beta cell inflammation in zebrafish identifies a natural product for human beta cell protection GSE123036 Transcriptome Analysis To assess the effect of chronic inflammation on the beta cells transcriptome we conducted RNA sequencing from 3 mpf zebrafish transgenic line Tgins:IL1B animals and WT siblings The total RNA from FACS sorted Beta cells was isolated using Quick RNA MicroPrep kit R1050 Zymo Research and following the manufacturer instructions. The sequencing was made on llumina HiSeq2500 in 2x75bp paired end mode. method Results:Two replicates for controls and two for IL1B expressing beta cells were sequenced. About 40 million sequence reads per sample were mapped to the Zebrafish genome. We identify around 19 thousand genes per sample. Approximately 6% of the genes were differentially expressed. 1 245 genes with a FDR of 5 showed a fold change =0.7 and adjusted p value <0.05. Conclusions: Hierarchical clustering by Pearson correlation of differentially expressed genes uncovered the expression of alpha cell related genes in beta cells. This provides a possible impairment of beta cell identity reflected in RNA expression profiles. Overall design: Beta cell mRNA profiles of 3 mpf wild type WT and Tgins:IL1B; cryaa:mCherry Zebrafihs were generated by deep sequencing in duplicate using llumina HiSeq2500.   pubmed:30679186   Con rep1 GSM3494231   source name:Pancreatic beta cells|genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type Con rep1 Illumina NextSeq Control/RTA2 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zebrafish genome GRCz10 using GSNAP from Ensembl gene annotation version 87 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Pancreatic beta cells   Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype/variation:Tgins:mKO|tissue:Pancreatic beta cells|age:3 mpf|genotype:wild type GSM3494231 GSM3494231: Con rep1; Danio rerio; RNA Seq GSM3494231   1 Beta cell isolated from islets were sorted and analyzed using FACS Aria II BD Bioscience. For dissociation islets were collected in PBS chilled on ice. post one washing with ice cold PBS islets were dissociated into single cells by incubation in TrypLE ThermoFisher 12563029 with 0.1% Pluronic F 68 ThermoFisher 24040032 at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation TrypLE was inactivated with 10% FBS and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re suspended in 500 ml of HBSS without xxx+ Mg2++0.1% Pluronic F 68. To remove debris the solution was passed over a 30 mm cell filter Miltenyi Biotec 130 041 407. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3494231 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP171016     L19372_Track-47628_R1.fastq.gz fastq 3743010792.0 49250142.0 GSM3494231 r1 0:76 A:1081119100;C:816543927;G:821868656;T:1023236057;N:243052 76       1081119100 816543927 821868656 1023236057 243052 SRX5073699 SRS4087525 SRA815642 GEO Ninov, CRTD 1 0.87612   0.16984   0.7684   0.57882   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2018-11-28 Adult Adult Pancreas Endocrine System
51051 51051 SRR8456909 SRX5263565 SRS4264370 SRP180299 PRJNA515911 Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish GSE125354 Transcriptome Analysis Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish   pubmed:31324766   alms1MUT 2 GSM3569389   tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf alms1MUT 2 trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set beta cells   single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf GSM3569389 GSM3569389: alms1MUT 2; Danio rerio; RNA Seq GSM3569389   1 single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  GEO Accession:GSM3569389 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP180299     alms1MUT-2_S204_R1_001.fastq.gz alms1MUT-2_S204_R2_001.fastq.gz fastq fastq 34706891262.0 114923481.0 GSM3569389 r1 0:151 1:151 A:9976818172;C:7360068941;G:7101573916;T:10265591911;N:2838322 151 151     9976818172 7360068941 7101573916 10265591911 2838322 SRX5263565 SRS4264370 SRA836454 GEO Medicine, University of Maryland School of Medicine 2 0.87723 0.87816 0.52783 0.53313 0.6729 0.69288 0.50497 0.5044 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United States 2019-01-18 Larval Larval Pancreas Endocrine System
51052 51052 SRR8456908 SRX5263564 SRS4264369 SRP180299 PRJNA515911 Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish GSE125354 Transcriptome Analysis Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish   pubmed:31324766   alms1MUT 1 GSM3569388   tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf alms1MUT 1 trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set beta cells   single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf GSM3569388 GSM3569388: alms1MUT 1; Danio rerio; RNA Seq GSM3569388   1 single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  GEO Accession:GSM3569388 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP180299     alms1MUT-1_S203_R1_001.fastq.gz alms1MUT-1_S203_R2_001.fastq.gz fastq fastq 31132041158.0 103086229.0 GSM3569388 r1 0:151 1:151 A:8977930028;C:6567587111;G:6338188683;T:9245824930;N:2510406 151 151     8977930028 6567587111 6338188683 9245824930 2510406 SRX5263564 SRS4264369 SRA836454 GEO Medicine, University of Maryland School of Medicine 2 0.87391 0.87469 0.49807 0.50313 0.68947 0.70449 0.51756 0.50827 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United States 2019-01-18 Larval Larval Pancreas Endocrine System
51053 51053 SRR8456907 SRX5263563 SRS4264368 SRP180299 PRJNA515911 Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish GSE125354 Transcriptome Analysis Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish   pubmed:31324766   WT 2 GSM3569387   tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf WT 2 trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set beta cells   single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf GSM3569387 GSM3569387: WT 2; Danio rerio; RNA Seq GSM3569387   1 single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  GEO Accession:GSM3569387 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP180299     WT-2_S202_R1_001.fastq.gz WT-2_S202_R2_001.fastq.gz fastq fastq 33558516632.0 111120916.0 GSM3569387 r1 0:151 1:151 A:9387420547;C:7359835200;G:7201488528;T:9607046373;N:2725984 151 151     9387420547 7359835200 7201488528 9607046373 2725984 SRX5263563 SRS4264368 SRA836454 GEO Medicine, University of Maryland School of Medicine 2 0.90113 0.9024 0.21941 0.22244 0.69572 0.70621 0.51483 0.51186 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United States 2019-01-18 Larval Larval Pancreas Endocrine System
51054 51054 SRR8456906 SRX5263562 SRS4264367 SRP180299 PRJNA515911 Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish GSE125354 Transcriptome Analysis Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish   pubmed:31324766   WT 1 GSM3569386   tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf WT 1 trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set beta cells   single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf GSM3569386 GSM3569386: WT 1; Danio rerio; RNA Seq GSM3569386   1 single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices.  GEO Accession:GSM3569386 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP180299     WT-1_S201_R1_001.fastq.gz WT-1_S201_R2_001.fastq.gz fastq fastq 35627069558.0 117970429.0 GSM3569386 r1 0:151 1:151 A:9789934413;C:8039430934;G:7849037733;T:9945758380;N:2908098 151 151     9789934413 8039430934 7849037733 9945758380 2908098 SRX5263562 SRS4264367 SRA836454 GEO Medicine, University of Maryland School of Medicine 2 0.91881 0.91874 0.23468 0.24084 0.66616 0.67969 0.46826 0.46848 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera bulk unknown unknown   United States 2019-01-18 Larval Larval Pancreas Endocrine System
64122 64122 SRR14272168 SRX10633820 SRS8730202 SRP315319 PRJNA722925 Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation PRJNA722925 Other Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.       Pancreas islets Pancreas islet 6dpf B2 Pancreas islets Islet 6d B2 AGN000787   strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000684|replicate ref:AGN000787|replicate order:2|BioSampleModel:Model organism or animal                 Pancreas islets Pancreas islet 6dpf B2 AGR001074 AGR001074 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP315319     AGR001074_R1.fastq.gz fastq 467368080.0 6149580.0 AGR001074 R1.fastq.gz 0:76 1:0 A:144866246;C:90980862;G:90828673;T:140671264;N:21035 76 0     144866246 90980862 90828673 140671264 21035 SRX10633820 SRS8730202 SRA1220217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.86223   0.47625   0.68556   0.52132   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2021-04-19 Larval Larval Pancreas Endocrine System
64123 64123 SRR14272169 SRX10633819 SRS8730201 SRP315319 PRJNA722925 Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation PRJNA722925 Other Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.       Pancreas islets Pancreas islet 6dpf B1 Pancreas islets Islet 6d B1 AGN000786   strain:TU/AB|age:not applicable|dev stage:Day 6|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000684|replicate ref:AGN000786|replicate order:1|BioSampleModel:Model organism or animal                 Pancreas islets Pancreas islet 6dpf B1 AGR001073 AGR001073 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP315319     AGR001073_R1.fastq.gz fastq 592506792.0 7796142.0 AGR001073 R1.fastq.gz 0:76 1:0 A:179281934;C:120318002;G:119990438;T:172891644;N:24774 76 0     179281934 120318002 119990438 172891644 24774 SRX10633819 SRS8730201 SRA1220217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.84252   0.35277   0.69219   0.54723   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2021-04-19 Larval Larval Pancreas Endocrine System
64128 64128 SRR14272174 SRX10633814 SRS8730196 SRP315319 PRJNA722925 Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation PRJNA722925 Other Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.       Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2 Pancreas islets Islet SST b cell abt 4d B2 AGN000782   strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000680|replicate ref:AGN000782|replicate order:2|BioSampleModel:Model organism or animal                 Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B2 AGR001070 AGR001070 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP315319     AGR001070_R1.fastq.gz fastq 481320616.0 6333166.0 AGR001070 R1.fastq.gz 0:76 1:0 A:151409804;C:91026556;G:90673968;T:148189727;N:20561 76 0     151409804 91026556 90673968 148189727 20561 SRX10633814 SRS8730196 SRA1220217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.82954   0.59765   0.75538   0.53049   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2021-04-19 Larval Larval Pancreas Endocrine System
64129 64129 SRR14272175 SRX10633813 SRS8730195 SRP315319 PRJNA722925 Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation PRJNA722925 Other Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.       Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1 Pancreas islets Islet SST b cell abt 4d B1 AGN000781   strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|treatment:metronidazole|molecule:mRNA|selection:pA|sample ref:AGS000680|replicate ref:AGN000781|replicate order:1|BioSampleModel:Model organism or animal                 Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP beta cell ablation B1 AGR001069 AGR001069 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP315319     AGR001069_R1.fastq.gz fastq 379230956.0 4989881.0 AGR001069 R1.fastq.gz 0:76 1:0 A:116227158;C:75587948;G:75371178;T:112027929;N:16743 76 0     116227158 75587948 75371178 112027929 16743 SRX10633813 SRS8730195 SRA1220217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.87385   0.38949   0.69242   0.47061   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2021-04-19 Larval Larval Pancreas Endocrine System
64133 64133 SRR14272179 SRX10633809 SRS8730192 SRP315319 PRJNA722925 Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation PRJNA722925 Other Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.       Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B2 Pancreas islets Islet SST 4d B2 AGN000780   strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000678|replicate ref:AGN000780|replicate order:2|BioSampleModel:Model organism or animal                 Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B2 AGR001068 AGR001068 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP315319     AGR001068_R1.fastq.gz fastq 1025641204.0 13495279.0 AGR001068 R1.fastq.gz 0:76 1:0 A:313399325;C:201992871;G:202026959;T:308179140;N:42909 76 0     313399325 201992871 202026959 308179140 42909 SRX10633809 SRS8730192 SRA1220217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.8692   0.47406   0.68081   0.54006   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2021-04-19 Larval Larval Pancreas Endocrine System
64134 64134 SRR14272180 SRX10633808 SRS8730191 SRP315319 PRJNA722925 Reinforcing one carbon metabolism via folic acid/Folr1 promotes beta cell differentiation PRJNA722925 Other Diabetes can be caused by an insufficiency in beta cell mass. Here we performed a genetic screen in a zebrafish model of beta cell loss to identify pathways promoting beta cell regeneration. We found that both folate receptor 1 folr1 overexpression and treatment with folinic acid stimulated beta cell differentiation in zebrafish. Treatment with folinic acid also stimulated beta cell differentiation in cultures of neonatal pig islets showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets the increased beta cell differentiation originated from ductal cells. Mechanistically comparative metabolomic analysis of zebrafish with/without xxx cell ablation and with/without xxx acid treatment indicated beta cell regeneration could be attributed to changes in the pyrimidine carnitine and serine pathways. Overall our results suggest evolutionarily conserved and previously unknown roles for folic acid and one carbon metabolism in the generation of beta cells.       Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B1 Pancreas islets Islet SST 4d B1 AGN000779   strain:TU/AB|age:not applicable|dev stage:Day 4|sex:pooled male and female|tissue:pancreas|molecule:mRNA|selection:pA|sample ref:AGS000678|replicate ref:AGN000779|replicate order:1|BioSampleModel:Model organism or animal                 Pancreas islets Pancreas islet 4dpf somatostatin transgene sst2:RFP B1 AGR001067 AGR001067 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP315319     AGR001067_R1.fastq.gz fastq 645391392.0 8491992.0 AGR001067 R1.fastq.gz 0:76 1:0 A:198297729;C:127050955;G:126777924;T:193238145;N:26639 76 0     198297729 127050955 126777924 193238145 26639 SRX10633808 SRS8730191 SRA1220217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.85746   0.50636   0.68286   0.48271   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2021-04-19 Larval Larval Pancreas Endocrine System
71089 71089 SRR21237242 SRX17246664 SRS14811789 SRP394370 PRJNA874056 Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish GSE212124 Transcriptome Analysis To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation   pubmed:39383064   MTZ2 GSM6509761   source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole MTZ2 sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample pancreas Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole GSM6509761 GSM6509761: MTZ2; Danio rerio; RNA Seq GSM6509761 r1 GSM6509761 1 Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP394370     IM_5_TAAGGCGA_L008_R2_001.fastq.gz IM_5_TAAGGCGA_L008_R1_001.fastq.gz fastq fastq 15325310144.0 75867872.0 GSM6509761 r1 0:101 1:101 A:4269635088;C:3380943498;G:3260211685;T:4413526478;N:993395 101 101     4269635088 3380943498 3260211685 4413526478 993395 SRX17246664 SRS14811789 SRA1485636 Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège 2 0.88443 0.88447 0.11507 0.11596 0.76686 0.7683 0.54694 0.55044 101 101 B B biological fallback assumption illumina nextseq full_length poly_a nextera bulk unknown unknown   Belgium 2022-08-26 Adult Adult Pancreas Endocrine System
71090 71090 SRR21237243 SRX17246663 SRS14811788 SRP394370 PRJNA874056 Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish GSE212124 Transcriptome Analysis To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation   pubmed:39383064   MTZ3 GSM6509762   source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole MTZ3 sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample pancreas Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole GSM6509762 GSM6509762: MTZ3; Danio rerio; RNA Seq GSM6509762 r1 GSM6509762 1 Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP394370     IM_6_CGTACTAG_L008_R2_001.fastq.gz IM_6_CGTACTAG_L008_R1_001.fastq.gz fastq fastq 19255819276.0 95325838.0 GSM6509762 r1 0:101 1:101 A:5280171088;C:4359058370;G:4172558504;T:5442855832;N:1175482 101 101     5280171088 4359058370 4172558504 5442855832 1175482 SRX17246663 SRS14811788 SRA1485636 Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège 2 0.90632 0.90614 0.08652 0.08772 0.76534 0.76696 0.52454 0.52158 101 101 B B biological fallback assumption illumina nextseq full_length poly_a nextera bulk unknown unknown   Belgium 2022-08-26 Adult Adult Pancreas Endocrine System
71091 71091 SRR21237244 SRX17246662 SRS14811787 SRP394370 PRJNA874056 Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish GSE212124 Transcriptome Analysis To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation   pubmed:39383064   MTZ1 GSM6509760   source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole MTZ1 sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample pancreas Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole GSM6509760 GSM6509760: MTZ1; Danio rerio; RNA Seq GSM6509760 r1 GSM6509760 1 Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP394370     IM_2_CGTACTAG_L006_R1_001.fastq.gz IM_2_CGTACTAG_L006_R2_001.fastq.gz fastq fastq 17015359304.0 84234452.0 GSM6509760 r1 0:101 1:101 A:4643492769;C:3861165659;G:3730150815;T:4779151147;N:1398914 101 101     4643492769 3861165659 3730150815 4779151147 1398914 SRX17246662 SRS14811787 SRA1485636 Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège 2 0.90217 0.90221 0.08047 0.08087 0.7651 0.76696 0.52075 0.53178 101 101 B B biological fallback assumption illumina nextseq full_length poly_a nextera bulk unknown unknown   Belgium 2022-08-26 Adult Adult Pancreas Endocrine System
71092 71092 SRR21237245 SRX17246661 SRS14811786 SRP394370 PRJNA874056 Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish GSE212124 Transcriptome Analysis To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation   pubmed:39383064   Ductal3 GSM6509759   source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO Ductal3 sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample pancreas Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO GSM6509759 GSM6509759: Ductal3; Danio rerio; RNA Seq GSM6509759 r1 GSM6509759 1 Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP394370     IM_4_CGTACTAG_L007_R2_001.fastq.gz IM_4_CGTACTAG_L007_R1_001.fastq.gz fastq fastq 17851670816.0 88374608.0 GSM6509759 r1 0:101 1:101 A:5161409723;C:3739347454;G:3476991371;T:5472775357;N:1146911 101 101     5161409723 3739347454 3476991371 5472775357 1146911 SRX17246661 SRS14811786 SRA1485636 Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège 2 0.85539 0.85497 0.14301 0.14391 0.78825 0.79115 0.52575 0.53365 101 101 B B biological fallback assumption illumina nextseq full_length poly_a nextera bulk unknown unknown   Belgium 2022-08-26 Adult Adult Pancreas Endocrine System
71093 71093 SRR21237246 SRX17246660 SRS14811785 SRP394370 PRJNA874056 Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish GSE212124 Transcriptome Analysis To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation   pubmed:39383064   Ductal2 GSM6509758   source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO Ductal2 sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample pancreas Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO GSM6509758 GSM6509758: Ductal2; Danio rerio; RNA Seq GSM6509758 r1 GSM6509758 1 Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP394370     IM_3_TAAGGCGA_L007_R1_001.fastq.gz IM_3_TAAGGCGA_L007_R2_001.fastq.gz fastq fastq 19081820314.0 94464457.0 GSM6509758 r1 0:101 1:101 A:5371144134;C:4166520026;G:3947780866;T:5595082921;N:1292367 101 101     5371144134 4166520026 3947780866 5595082921 1292367 SRX17246660 SRS14811785 SRA1485636 Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège 2 0.88865 0.88865 0.14515 0.14711 0.7768 0.77857 0.53802 0.54651 101 101 B B biological fallback assumption illumina nextseq full_length poly_a nextera bulk unknown unknown   Belgium 2022-08-26 Adult Adult Pancreas Endocrine System
71094 71094 SRR21237247 SRX17246659 SRS14811784 SRP394370 PRJNA874056 Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish GSE212124 Transcriptome Analysis To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation   pubmed:39383064   Ductal1 GSM6509757   source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO Ductal1 sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample pancreas Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO GSM6509757 GSM6509757: Ductal1; Danio rerio; RNA Seq GSM6509757 r1 GSM6509757 1 Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP394370     IM_1_TCCTGAGC_L006_R1_001.fastq.gz IM_1_TCCTGAGC_L006_R2_001.fastq.gz fastq fastq 17515315364.0 86709482.0 GSM6509757 r1 0:101 1:101 A:4877105284;C:3850259782;G:3695070211;T:5091356227;N:1523860 101 101     4877105284 3850259782 3695070211 5091356227 1523860 SRX17246659 SRS14811784 SRA1485636 Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège 2 0.87916 0.87844 0.08877 0.08911 0.80022 0.80316 0.54436 0.54865 101 101 B B biological fallback assumption illumina nextseq full_length poly_a nextera bulk unknown unknown   Belgium 2022-08-26 Adult Adult Pancreas Endocrine System

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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");;