rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 321,ERR977589,ERX1054572,ERS805778,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Delta cells R3,SAMEA3498629,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498629|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:34|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:34,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:489 14,Delta R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B176_SSTcells-03122013_CAGATC_L001_R1_001.fastq.gz NGS14-B176_SSTcells-03122013_CAGATC_L001_R2_001.fastq.gz,fastq fastq,17691597128.0,87582164.0,ena RUN GIGA R University of Liege 05 08 2015 16:56:42:489 14,0:101 1:101,A:4843643109;C:3683816237;G:3736882877;T:5332210638;N:95044267,101,101,,,4843643109,3683816237,3736882877,5332210638,95044267,ERX1054572,ERS805778,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.92685,0.84146,0.10249,0.11723,0.76532,0.78309,0.39721,0.43714,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System 330,ERR977580,ERX1054563,ERS805769,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R3,SAMEA3498620,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498620|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:25|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:25,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 5,Beta R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B174_Betacells-03122013_GCCAAT_L002_R1_001.fastq.gz NGS14-B174_Betacells-03122013_GCCAAT_L002_R2_001.fastq.gz,fastq fastq,17625660086.0,87255743.0,ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 5,0:101 1:101,A:4840276660;C:3724973884;G:3755195525;T:5214977933;N:90236084,101,101,,,4840276660,3724973884,3755195525,5214977933,90236084,ERX1054563,ERS805769,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90631,0.8718,0.11791,0.11942,0.76203,0.77638,0.53654,0.49457,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System 331,ERR977579,ERX1054562,ERS805768,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R2 2,SAMEA3498619,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498619|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:24|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:24,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 4,Beta R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell2_A026_ATGTCA_L004_R1_001.fastq.gz BetaCell2_A026_ATGTCA_L004_R2_001.fastq.gz,fastq fastq,8532015198.0,42237699.0,ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 4,0:101 1:101,A:2314776471;C:1823939144;G:1839244845;T:2552984556;N:1070182,101,101,,,2314776471,1823939144,1839244845,2552984556,1070182,ERX1054562,ERS805768,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.69844,0.57999,0.09124,0.07501,0.80876,0.82964,0.56023,0.5159,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System 332,ERR977578,ERX1054561,ERS805767,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R2 1,SAMEA3498618,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498618|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:23|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:23,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 3,Beta R2 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell_ATGTCA_L005_R1_001.fastq.gz BetaCell_ATGTCA_L005_R2_001.fastq.gz,fastq fastq,3250611068.0,16092134.0,ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 3,0:101 1:101,A:854826460;C:691024995;G:695294721;T:954934438;N:54530454,101,101,,,854826460,691024995,695294721,954934438,54530454,ERX1054561,ERS805767,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.67496,0.53873,0.08771,0.06606,0.80969,0.83433,0.56231,0.51717,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System 333,ERR977577,ERX1054560,ERS805766,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R1 2,SAMEA3498617,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498617|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:22|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:22,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:487 2,Beta R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell1_A003_GTCCGC_L004_R1_001.fastq.gz BetaCell1_A003_GTCCGC_L004_R2_001.fastq.gz,fastq fastq,3765102038.0,18639119.0,ena RUN GIGA R University of Liege 05 08 2015 16:56:42:487 2,0:101 1:101,A:1050226787;C:789381360;G:801049952;T:1123973291;N:470648,101,101,,,1050226787,789381360,801049952,1123973291,470648,ERX1054560,ERS805766,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90456,0.86125,0.12934,0.13194,0.77721,0.79109,0.56708,0.53213,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System 334,ERR977576,ERX1054559,ERS805765,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar alpha beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a ß and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R1 1,SAMEA3498616,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498616|INSDC center alias:GIGA R University of Liege|INSDC center name:GIGA R University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:21|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:21,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R University of Liege 05 08 2015 16:56:42:486 1,Beta R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCells_30000_GTCCGC_L008_R1_001.fastq.gz BetaCells_30000_GTCCGC_L008_R2_001.fastq.gz,fastq fastq,10597717092.0,52463946.0,ena RUN GIGA R University of Liege 05 08 2015 16:56:42:486 1,0:101 1:101,A:2951812422;C:2213949786;G:2252957090;T:3178649938;N:347856,101,101,,,2951812422,2213949786,2252957090,3178649938,347856,ERX1054559,ERS805765,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90302,0.84857,0.12843,0.12749,0.77745,0.79157,0.56129,0.52011,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System 44907,SRR6293905,SRX3395016,SRS2689202,SRP125042,PRJNA418467,Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish,GSE106938,Transcriptome Analysis,Individual organisms age at different rates however it remains unclear how aging alters the properties of individual cells. Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age. Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress inhibition of growth factor signaling and inflammation including NF kB signaling. Using a reporter line we show that NF kB signaling is indeed activated heterogeneously with age. Notably beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity. Furthermore NF kB signalinghigh beta cells from younger islets upregulate socs2 a gene naturally expressed in beta cells from older islets. In turn socs2 can inhibit proliferation cell autonomously. NF kB activation correlates with the recruitment of tnfa expressing immune cells pointing towards a role for the islet microenvironment in this activity. We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome GRCz10 using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.,,pubmed:29624168,,1ypf rep2,GSM2857832,,tissue:beta cells|age:1 year|strain:Tgins:BB1.0L,1ypf rep2,Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count,beta cells,,FACS llumina HiSeq2500 in 2x75bp paired end mode,,age:1 year|strain:Tgins:BB1.0L,GSM2857832,GSM2857832: 1ypf rep2; Danio rerio; RNA Seq,GSM2857832,,1,FACS llumina HiSeq2500 in 2x75bp paired end mode,GEO Accession:GSM2857832,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125042,,,L10760_Track-31237_R1.fastq.gz L10760_Track-31237_R2.fastq.gz,fastq fastq,5627077088.0,37020244.0,GSM2857832 r1,0:76 1:76,A:1481195914;C:1302350910;G:1313408578;T:1524234346;N:5887340,76,76,,,1481195914,1302350910,1313408578,1524234346,5887340,SRX3395016,SRS2689202,SRA631121,GEO,"Ninov Lab, CRTD",2,0.84288,0.84015,0.15135,0.15241,0.75089,0.75436,0.60917,0.60027,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2017-11-15,Adult,Adult,Pancreas,Endocrine System 44908,SRR6293904,SRX3395015,SRS2689200,SRP125042,PRJNA418467,Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish,GSE106938,Transcriptome Analysis,Individual organisms age at different rates however it remains unclear how aging alters the properties of individual cells. Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age. Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress inhibition of growth factor signaling and inflammation including NF kB signaling. Using a reporter line we show that NF kB signaling is indeed activated heterogeneously with age. Notably beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity. Furthermore NF kB signalinghigh beta cells from younger islets upregulate socs2 a gene naturally expressed in beta cells from older islets. In turn socs2 can inhibit proliferation cell autonomously. NF kB activation correlates with the recruitment of tnfa expressing immune cells pointing towards a role for the islet microenvironment in this activity. We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome GRCz10 using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.,,pubmed:29624168,,1ypf rep1,GSM2857831,,tissue:beta cells|age:1 year|strain:Tgins:BB1.0L,1ypf rep1,Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count,beta cells,,FACS llumina HiSeq2500 in 2x75bp paired end mode,,age:1 year|strain:Tgins:BB1.0L,GSM2857831,GSM2857831: 1ypf rep1; Danio rerio; RNA Seq,GSM2857831,,1,FACS llumina HiSeq2500 in 2x75bp paired end mode,GEO Accession:GSM2857831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125042,,,L10759_Track-31236_R1.fastq.gz L10759_Track-31236_R2.fastq.gz,fastq fastq,5128054856.0,33737203.0,GSM2857831 r1,0:76 1:76,A:1350542699;C:1184925079;G:1197353068;T:1389942509;N:5291501,76,76,,,1350542699,1184925079,1197353068,1389942509,5291501,SRX3395015,SRS2689200,SRA631121,GEO,"Ninov Lab, CRTD",2,0.84827,0.85287,0.16376,0.1636,0.75645,0.75797,0.59534,0.59534,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2017-11-15,Adult,Adult,Pancreas,Endocrine System 44909,SRR6293903,SRX3395014,SRS2689199,SRP125042,PRJNA418467,Age related Islet Inflammation Marks the Proliferative Decline of Pancreatic Beta cells in Zebrafish,GSE106938,Transcriptome Analysis,Individual organisms age at different rates however it remains unclear how aging alters the properties of individual cells. Here we show that zebrafish pancreatic beta cells exhibit heterogeneity in both gene expression and proliferation with age. Individual beta cells show marked variability in transcripts involved in endoplasmic reticulum stress inhibition of growth factor signaling and inflammation including NF kB signaling. Using a reporter line we show that NF kB signaling is indeed activated heterogeneously with age. Notably beta cells with higher NF kB activity proliferate less compared to neighbors with lower activity. Furthermore NF kB signalinghigh beta cells from younger islets upregulate socs2 a gene naturally expressed in beta cells from older islets. In turn socs2 can inhibit proliferation cell autonomously. NF kB activation correlates with the recruitment of tnfa expressing immune cells pointing towards a role for the islet microenvironment in this activity. We propose that aging is heterogeneous across individual beta cells and identify NF kB signaling as a marker of heterogeneity. Overall design: We used fluorescence activated cell sorting FACS coupled with next generation RNA Sequencing to profile beta cells from 3 mpf and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta cells using Quick RNA MicroPrep kit R1050 Zymo Research. Sequencing was performed on llumina HiSeq2500 in 2x75bp paired end mode. Reads were splice aligned to the zebrafish genome GRCz10 using HISAT2. htseq count was used to assign reads to exons thus eventually getting counts per gene.,,pubmed:29624168,,3mpf rep1,GSM2857830,,tissue:beta cells|age:3 month|strain:Tgins:BB1.0L,3mpf rep1,Trimming using trim galore using default parameters Mapping using HISAT2 with default parameters Counts per gene generated using htseq count with default parameters sam files converted to bam using samtools Genome build: Zebrafish GRCz10 Supplementary files format and content: read counts were generated using htseq count,beta cells,,FACS llumina HiSeq2500 in 2x75bp paired end mode,,age:3 month|strain:Tgins:BB1.0L,GSM2857830,GSM2857830: 3mpf rep1; Danio rerio; RNA Seq,GSM2857830,,1,FACS llumina HiSeq2500 in 2x75bp paired end mode,GEO Accession:GSM2857830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125042,,,L10758_Track-31235_R1.fastq.gz L10758_Track-31235_R2.fastq.gz,fastq fastq,4259609848.0,28023749.0,GSM2857830 r1,0:76 1:76,A:1095866394;C:1004201489;G:1014981602;T:1140141196;N:4419167,76,76,,,1095866394,1004201489,1014981602,1140141196,4419167,SRX3395014,SRS2689199,SRA631121,GEO,"Ninov Lab, CRTD",2,0.87618,0.87022,0.1249,0.12602,0.76368,0.76469,0.65739,0.64564,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2017-11-15,Adult,Adult,Pancreas,Endocrine System 51051,SRR8456909,SRX5263565,SRS4264370,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,alms1MUT 2,GSM3569389,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,alms1MUT 2,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,GSM3569389,GSM3569389: alms1MUT 2; Danio rerio; RNA Seq,GSM3569389,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569389,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,alms1MUT-2_S204_R1_001.fastq.gz alms1MUT-2_S204_R2_001.fastq.gz,fastq fastq,34706891262.0,114923481.0,GSM3569389 r1,0:151 1:151,A:9976818172;C:7360068941;G:7101573916;T:10265591911;N:2838322,151,151,,,9976818172,7360068941,7101573916,10265591911,2838322,SRX5263565,SRS4264370,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.87723,0.87816,0.52783,0.53313,0.6729,0.69288,0.50497,0.5044,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System 51052,SRR8456908,SRX5263564,SRS4264369,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,alms1MUT 1,GSM3569388,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,alms1MUT 1,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:alms1 / |age:5 dpf,GSM3569388,GSM3569388: alms1MUT 1; Danio rerio; RNA Seq,GSM3569388,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569388,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,alms1MUT-1_S203_R1_001.fastq.gz alms1MUT-1_S203_R2_001.fastq.gz,fastq fastq,31132041158.0,103086229.0,GSM3569388 r1,0:151 1:151,A:8977930028;C:6567587111;G:6338188683;T:9245824930;N:2510406,151,151,,,8977930028,6567587111,6338188683,9245824930,2510406,SRX5263564,SRS4264369,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.87391,0.87469,0.49807,0.50313,0.68947,0.70449,0.51756,0.50827,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System 51053,SRR8456907,SRX5263563,SRS4264368,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,WT 2,GSM3569387,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,WT 2,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,GSM3569387,GSM3569387: WT 2; Danio rerio; RNA Seq,GSM3569387,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569387,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,WT-2_S202_R1_001.fastq.gz WT-2_S202_R2_001.fastq.gz,fastq fastq,33558516632.0,111120916.0,GSM3569387 r1,0:151 1:151,A:9387420547;C:7359835200;G:7201488528;T:9607046373;N:2725984,151,151,,,9387420547,7359835200,7201488528,9607046373,2725984,SRX5263563,SRS4264368,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.90113,0.9024,0.21941,0.22244,0.69572,0.70621,0.51483,0.51186,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System 51054,SRR8456906,SRX5263562,SRS4264367,SRP180299,PRJNA515911,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish,GSE125354,Transcriptome Analysis,Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish,,pubmed:31324766,,WT 1,GSM3569386,,tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,WT 1,trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set,beta cells,,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry,cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf,GSM3569386,GSM3569386: WT 1; Danio rerio; RNA Seq,GSM3569386,,1,single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. ,GEO Accession:GSM3569386,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP180299,,,WT-1_S201_R1_001.fastq.gz WT-1_S201_R2_001.fastq.gz,fastq fastq,35627069558.0,117970429.0,GSM3569386 r1,0:151 1:151,A:9789934413;C:8039430934;G:7849037733;T:9945758380;N:2908098,151,151,,,9789934413,8039430934,7849037733,9945758380,2908098,SRX5263562,SRS4264367,SRA836454,GEO,"Medicine, University of Maryland School of Medicine",2,0.91881,0.91874,0.23468,0.24084,0.66616,0.67969,0.46826,0.46848,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,bulk,unknown,unknown,,United States,2019-01-18,Larval,Larval,Pancreas,Endocrine System 71089,SRR21237242,SRX17246664,SRS14811789,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,MTZ2,GSM6509761,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,MTZ2,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,GSM6509761,GSM6509761: MTZ2; Danio rerio; RNA Seq,GSM6509761 r1,GSM6509761,1,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_5_TAAGGCGA_L008_R2_001.fastq.gz IM_5_TAAGGCGA_L008_R1_001.fastq.gz,fastq fastq,15325310144.0,75867872.0,GSM6509761 r1,0:101 1:101,A:4269635088;C:3380943498;G:3260211685;T:4413526478;N:993395,101,101,,,4269635088,3380943498,3260211685,4413526478,993395,SRX17246664,SRS14811789,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.88443,0.88447,0.11507,0.11596,0.76686,0.7683,0.54694,0.55044,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System 71090,SRR21237243,SRX17246663,SRS14811788,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,MTZ3,GSM6509762,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,MTZ3,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,GSM6509762,GSM6509762: MTZ3; Danio rerio; RNA Seq,GSM6509762 r1,GSM6509762,1,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_6_CGTACTAG_L008_R2_001.fastq.gz IM_6_CGTACTAG_L008_R1_001.fastq.gz,fastq fastq,19255819276.0,95325838.0,GSM6509762 r1,0:101 1:101,A:5280171088;C:4359058370;G:4172558504;T:5442855832;N:1175482,101,101,,,5280171088,4359058370,4172558504,5442855832,1175482,SRX17246663,SRS14811788,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.90632,0.90614,0.08652,0.08772,0.76534,0.76696,0.52454,0.52158,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System 71091,SRR21237244,SRX17246662,SRS14811787,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,MTZ1,GSM6509760,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,MTZ1,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole,GSM6509760,GSM6509760: MTZ1; Danio rerio; RNA Seq,GSM6509760 r1,GSM6509760,1,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_2_CGTACTAG_L006_R1_001.fastq.gz IM_2_CGTACTAG_L006_R2_001.fastq.gz,fastq fastq,17015359304.0,84234452.0,GSM6509760 r1,0:101 1:101,A:4643492769;C:3861165659;G:3730150815;T:4779151147;N:1398914,101,101,,,4643492769,3861165659,3730150815,4779151147,1398914,SRX17246662,SRS14811787,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.90217,0.90221,0.08047,0.08087,0.7651,0.76696,0.52075,0.53178,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System 71092,SRR21237245,SRX17246661,SRS14811786,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,Ductal3,GSM6509759,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,Ductal3,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,GSM6509759,GSM6509759: Ductal3; Danio rerio; RNA Seq,GSM6509759 r1,GSM6509759,1,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_4_CGTACTAG_L007_R2_001.fastq.gz IM_4_CGTACTAG_L007_R1_001.fastq.gz,fastq fastq,17851670816.0,88374608.0,GSM6509759 r1,0:101 1:101,A:5161409723;C:3739347454;G:3476991371;T:5472775357;N:1146911,101,101,,,5161409723,3739347454,3476991371,5472775357,1146911,SRX17246661,SRS14811786,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.85539,0.85497,0.14301,0.14391,0.78825,0.79115,0.52575,0.53365,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System 71093,SRR21237246,SRX17246660,SRS14811785,SRP394370,PRJNA874056,Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish,GSE212124,Transcriptome Analysis,To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation,,pubmed:39383064,,Ductal2,GSM6509758,,source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,Ductal2,sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,pancreas,Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO,GSM6509758,GSM6509758: Ductal2; Danio rerio; RNA Seq,GSM6509758 r1,GSM6509758,1,Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP394370,,,IM_3_TAAGGCGA_L007_R1_001.fastq.gz IM_3_TAAGGCGA_L007_R2_001.fastq.gz,fastq fastq,19081820314.0,94464457.0,GSM6509758 r1,0:101 1:101,A:5371144134;C:4166520026;G:3947780866;T:5595082921;N:1292367,101,101,,,5371144134,4166520026,3947780866,5595082921,1292367,SRX17246660,SRS14811785,SRA1485636,"Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège","Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège",2,0.88865,0.88865,0.14515,0.14711,0.7768,0.77857,0.53802,0.54651,101,101,B,B,biological fallback assumption,illumina,nextseq,full_length,poly_a,nextera,bulk,unknown,unknown,,Belgium,2022-08-26,Adult,Adult,Pancreas,Endocrine System 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