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
226,DRR162515,DRX153134,DRS083195,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 39 mpf zebrafish replicate4,SAMD00152463,,sample name:h39 5|age:39 month|biological replicate:4|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152463,DRX153134,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152463,,,,752785200.0,3763926.0,DRR162515,0:100 1:100,A:211753297;C:164230605;G:164002975;T:211653858;N:1144465,100,100,,,211753297,164230605,164002975,211653858,1144465,DRX153134,DRS083195,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94694,0.92403,0.08673,0.0834,0.76676,0.77494,0.55153,0.55428,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
227,DRR162514,DRX153133,DRS083194,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 39 mpf zebrafish replicate3,SAMD00152462,,sample name:h39 4|age:39 month|biological replicate:3|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152462,DRX153133,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152462,,,,679062000.0,3395310.0,DRR162514,0:100 1:100,A:196564583;C:142498995;G:143087462;T:195785946;N:1125014,100,100,,,196564583,142498995,143087462,195785946,1125014,DRX153133,DRS083194,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93382,0.90845,0.09509,0.09064,0.74959,0.75716,0.54651,0.55443,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
228,DRR162513,DRX153132,DRS083193,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 39 mpf zebrafish replicate2,SAMD00152461,,sample name:h39 3|age:39 month|biological replicate:2|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152461,DRX153132,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152461,,,,820363600.0,4101818.0,DRR162513,0:100 1:100,A:216665257;C:194340343;G:194565546;T:214750864;N:41590,100,100,,,216665257,194340343,194565546,214750864,41590,DRX153132,DRS083193,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96835,0.9597,0.05737,0.05723,0.77518,0.78977,0.52379,0.52345,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
229,DRR162512,DRX153131,DRS083192,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 39 mpf zebrafish replicate1,SAMD00152460,,sample name:h39 2|age:39 month|biological replicate:1|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152460,DRX153131,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152460,,,,865257400.0,4326287.0,DRR162512,0:100 1:100,A:232463535;C:201007012;G:201960678;T:229782957;N:43218,100,100,,,232463535,201007012,201960678,229782957,43218,DRX153131,DRS083192,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96533,0.95132,0.05078,0.04891,0.79961,0.80204,0.5113,0.51569,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
230,DRR162511,DRX153130,DRS083191,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 16 mpf zebrafish replicate5,SAMD00152459,,sample name:h16 5|age:16 month|biological replicate:5|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152459,DRX153130,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152459,,,,719278200.0,3596391.0,DRR162511,0:100 1:100,A:208319036;C:151385486;G:151714770;T:207822080;N:36828,100,100,,,208319036,151385486,151714770,207822080,36828,DRX153130,DRS083191,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95229,0.95465,0.0764,0.07543,0.80056,0.80229,0.51533,0.5793,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
231,DRR162510,DRX153129,DRS083190,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 16 mpf zebrafish replicate4,SAMD00152458,,sample name:h16 4|age:16 month|biological replicate:4|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152458,DRX153129,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152458,,,,826575600.0,4132878.0,DRR162510,0:100 1:100,A:248945884;C:164298731;G:163783086;T:249505745;N:42154,100,100,,,248945884,164298731,163783086,249505745,42154,DRX153129,DRS083190,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92443,0.9204,0.12773,0.1248,0.75702,0.75948,0.55913,0.57701,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
232,DRR162509,DRX153128,DRS083189,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 16 mpf zebrafish replicate3,SAMD00152457,,sample name:h16 3|age:16 month|biological replicate:3|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152457,DRX153128,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152457,,,,1094115600.0,5470578.0,DRR162509,0:100 1:100,A:323187964;C:223739793;G:223873492;T:323258173;N:56178,100,100,,,323187964,223739793,223873492,323258173,56178,DRX153128,DRS083189,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94683,0.94429,0.08329,0.08231,0.78845,0.78875,0.59669,0.60756,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
233,DRR162508,DRX153127,DRS083188,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 16 mpf zebrafish replicate2,SAMD00152456,,sample name:h16 2|age:16 month|biological replicate:2|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152456,DRX153127,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152456,,,,1020794600.0,5103973.0,DRR162508,0:100 1:100,A:308506490;C:201790189;G:201599005;T:308845325;N:53591,100,100,,,308506490,201790189,201599005,308845325,53591,DRX153127,DRS083188,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93523,0.93011,0.10853,0.10682,0.77727,0.77841,0.5927,0.59624,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
234,DRR162507,DRX153126,DRS083187,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 16 mpf zebrafish replicate1,SAMD00152455,,sample name:h16 1|age:16 month|biological replicate:1|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152455,DRX153126,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152455,,,,733044200.0,3665221.0,DRR162507,0:100 1:100,A:217522605;C:148795881;G:149576712;T:217109635;N:39367,100,100,,,217522605,148795881,149576712,217109635,39367,DRX153126,DRS083187,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94337,0.92685,0.08628,0.08365,0.78147,0.78366,0.61098,0.61073,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
235,DRR162506,DRX153125,DRS083186,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 7 mpf zebrafish replicate5,SAMD00152454,,sample name:h07 5|age:7 month|biological replicate:5|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152454,DRX153125,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152454,,,,979233200.0,4896166.0,DRR162506,0:100 1:100,A:249561707;C:239388088;G:240240872;T:248407989;N:1634544,100,100,,,249561707,239388088,240240872,248407989,1634544,DRX153125,DRS083186,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9639,0.93711,0.08232,0.07857,0.7835,0.79198,0.52539,0.51656,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
236,DRR162505,DRX153124,DRS083185,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 7 mpf zebrafish replicate4,SAMD00152453,,sample name:h07 4|age:7 month|biological replicate:4|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152453,DRX153124,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152453,,,,633922400.0,3169612.0,DRR162505,0:100 1:100,A:158236352;C:158464487;G:159505789;T:156692659;N:1023113,100,100,,,158236352,158464487,159505789,156692659,1023113,DRX153124,DRS083185,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97351,0.94642,0.06401,0.06072,0.83721,0.84532,0.52177,0.5279,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
237,DRR162504,DRX153123,DRS083184,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 7 mpf zebrafish replicate3,SAMD00152452,,sample name:h07 3|age:7 month|biological replicate:3|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152452,DRX153123,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152452,,,,3134971400.0,15674857.0,DRR162504,0:100 1:100,A:848586113;C:717201130;G:718012934;T:846124340;N:5046883,100,100,,,848586113,717201130,718012934,846124340,5046883,DRX153123,DRS083184,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95766,0.93244,0.06284,0.06048,0.7767,0.78595,0.5246,0.53241,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
238,DRR162503,DRX153122,DRS083183,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 7 mpf zebrafish replicate2,SAMD00152451,,sample name:h07 2|age:7 month|biological replicate:2|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152451,DRX153122,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152451,,,,1128933600.0,5644668.0,DRR162503,0:100 1:100,A:298341135;C:265514569;G:266315284;T:296956092;N:1806520,100,100,,,298341135,265514569,266315284,296956092,1806520,DRX153122,DRS083183,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96447,0.94022,0.07383,0.07032,0.79295,0.80075,0.5553,0.54794,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
239,DRR162502,DRX153121,DRS083182,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,heart sample from 7 mpf zebrafish replicate1,SAMD00152450,,sample name:h07 1|age:7 month|biological replicate:1|tissue:heart,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152450,DRX153121,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152450,,,,1104589000.0,5522945.0,DRR162502,0:100 1:100,A:296710605;C:254979238;G:256772800;T:294385639;N:1740718,100,100,,,296710605,254979238,256772800,294385639,1740718,DRX153121,DRS083182,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9561,0.92652,0.05819,0.05627,0.77914,0.78729,0.49578,0.52012,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Heart,Cardiovascular System
4359,ERR1427424,ERX1497956,ERS1183258,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#91,SAMEA4012148,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012148|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#91|broker name:ArrayExpress|common name:zebrafish|fsc:25859|gfp:119|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#91|ssc:10090|tissue:Heart|well:C12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#91,LCK 7#91,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25859:fsc|Experimental Factor: 10090:ssc|Experimental Factor: 119:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_91_mod.bam LCK_7_91.cram,bam cram,,,E MTAB 4617:LCK 7#91,0:125 1:125,A:115117295;C:110480558;G:102056870;T:121829131;N:52646,125,125,,,115117295,110480558,102056870,121829131,52646,ERX1497956,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.2053,0.20024,0.06111,0.05989,0.98019,0.98058,0.56103,0.56868,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4360,ERR1427423,ERX1497955,ERS1183257,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#90,SAMEA4012147,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012147|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#90|broker name:ArrayExpress|common name:zebrafish|fsc:22987|gfp:178|individual:2|pi:6|plate:7|sample name:E MTAB 4617:LCK 7#90|ssc:6327|tissue:Heart|well:B12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#90,LCK 7#90,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 22987:fsc|Experimental Factor: 6327:ssc|Experimental Factor: 178:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_90_mod.bam LCK_7_90.cram,bam cram,,,E MTAB 4617:LCK 7#90,0:125 1:125,A:106342222;C:98049090;G:91971650;T:111243138;N:46400,125,125,,,106342222,98049090,91971650,111243138,46400,ERX1497955,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.2785,0.27322,0.08361,0.08291,0.97619,0.97703,0.60537,0.61379,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4361,ERR1427422,ERX1497954,ERS1183256,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#9,SAMEA4012146,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012146|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#9|broker name:ArrayExpress|common name:zebrafish|fsc:24861|gfp:531|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#9|ssc:5852|tissue:Heart|well:A2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#9,LCK 7#9,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 24861:fsc|Experimental Factor: 5852:ssc|Experimental Factor: 531:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_9_mod.bam LCK_7_9.cram,bam cram,,,E MTAB 4617:LCK 7#9,0:125 1:125,A:99732231;C:96455828;G:89233454;T:105851298;N:47439,125,125,,,99732231,96455828,89233454,105851298,47439,ERX1497954,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.21894,0.21406,0.0599,0.05904,0.97861,0.97877,0.57755,0.57546,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4362,ERR1427421,ERX1497953,ERS1183255,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#89,SAMEA4012145,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012145|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#89|broker name:ArrayExpress|common name:zebrafish|fsc:26923|gfp:664|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#89|ssc:7976|tissue:Heart|well:A12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#89,LCK 7#89,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26923:fsc|Experimental Factor: 7976:ssc|Experimental Factor: 664:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_89_mod.bam LCK_7_89.cram,bam cram,,,E MTAB 4617:LCK 7#89,0:125 1:125,A:53847121;C:51852010;G:47816940;T:57047962;N:23717,125,125,,,53847121,51852010,47816940,57047962,23717,ERX1497953,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.22382,0.21939,0.05208,0.05177,0.97952,0.97979,0.49483,0.59346,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4368,ERR1427415,ERX1497947,ERS1183249,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#83,SAMEA4012139,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012139|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#83|broker name:ArrayExpress|common name:zebrafish|fsc:23855|gfp:97|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#83|ssc:7394|tissue:Heart|well:C11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#83,LCK 7#83,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23855:fsc|Experimental Factor: 7394:ssc|Experimental Factor: 97:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_83_mod.bam LCK_7_83.cram,bam cram,,,E MTAB 4617:LCK 7#83,0:125 1:125,A:73686338;C:69380167;G:63301440;T:77949626;N:35429,125,125,,,73686338,69380167,63301440,77949626,35429,ERX1497947,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.1643,0.16094,0.06354,0.06267,0.98526,0.98581,0.60921,0.60841,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4369,ERR1427414,ERX1497946,ERS1183248,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#82,SAMEA4012138,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012138|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#82|broker name:ArrayExpress|common name:zebrafish|fsc:27473|gfp:554|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#82|ssc:9625|tissue:Heart|well:B11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#82,LCK 7#82,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27473:fsc|Experimental Factor: 9625:ssc|Experimental Factor: 554:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_82_mod.bam LCK_7_82.cram,bam cram,,,E MTAB 4617:LCK 7#82,0:125 1:125,A:132306808;C:126337107;G:118115874;T:139760194;N:65267,125,125,,,132306808,126337107,118115874,139760194,65267,ERX1497946,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.18655,0.18247,0.05663,0.05588,0.97916,0.97918,0.57019,0.56851,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4370,ERR1427413,ERX1497945,ERS1183247,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#81,SAMEA4012137,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012137|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#81|broker name:ArrayExpress|common name:zebrafish|fsc:26381|gfp:492|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#81|ssc:6369|tissue:Heart|well:A11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#81,LCK 7#81,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26381:fsc|Experimental Factor: 6369:ssc|Experimental Factor: 492:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_81_mod.bam LCK_7_81.cram,bam cram,,,E MTAB 4617:LCK 7#81,0:125 1:125,A:49752056;C:47569625;G:43787172;T:52848426;N:21471,125,125,,,49752056,47569625,43787172,52848426,21471,ERX1497945,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.18831,0.18533,0.05553,0.05564,0.98076,0.98147,0.55231,0.5582,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4377,ERR1427406,ERX1497938,ERS1183240,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#75,SAMEA4012130,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012130|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#75|broker name:ArrayExpress|common name:zebrafish|fsc:29804|gfp:381|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#75|ssc:9855|tissue:Heart|well:C10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#75,LCK 7#75,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 29804:fsc|Experimental Factor: 9855:ssc|Experimental Factor: 381:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_75_mod.bam LCK_7_75.cram,bam cram,,,E MTAB 4617:LCK 7#75,0:125 1:125,A:215270392;C:173814423;G:161953517;T:222035470;N:96448,125,125,,,215270392,173814423,161953517,222035470,96448,ERX1497938,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.40731,0.4045,0.14845,0.14768,0.97908,0.97906,0.59339,0.61288,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4378,ERR1427405,ERX1497937,ERS1183239,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#74,SAMEA4012129,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012129|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#74|broker name:ArrayExpress|common name:zebrafish|fsc:27947|gfp:352|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#74|ssc:7917|tissue:Heart|well:B10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#74,LCK 7#74,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27947:fsc|Experimental Factor: 7917:ssc|Experimental Factor: 352:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_74_mod.bam LCK_7_74.cram,bam cram,,,E MTAB 4617:LCK 7#74,0:125 1:125,A:123931531;C:111767107;G:106439636;T:128665381;N:58095,125,125,,,123931531,111767107,106439636,128665381,58095,ERX1497937,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.24486,0.2405,0.06375,0.06316,0.97845,0.97938,0.55948,0.55443,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4379,ERR1427404,ERX1497936,ERS1183238,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#73,SAMEA4012128,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012128|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#73|broker name:ArrayExpress|common name:zebrafish|fsc:27976|gfp:511|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#73|ssc:9269|tissue:Heart|well:A10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#73,LCK 7#73,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27976:fsc|Experimental Factor: 9269:ssc|Experimental Factor: 511:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_73_mod.bam LCK_7_73.cram,bam cram,,,E MTAB 4617:LCK 7#73,0:125 1:125,A:47487658;C:44369011;G:41797745;T:49759850;N:22236,125,125,,,47487658,44369011,41797745,49759850,22236,ERX1497936,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.20054,0.19572,0.06216,0.06174,0.98141,0.98165,0.57621,0.56697,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4386,ERR1427397,ERX1497929,ERS1183231,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#67,SAMEA4012121,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012121|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#67|broker name:ArrayExpress|common name:zebrafish|fsc:27129|gfp:522|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#67|ssc:7035|tissue:Heart|well:C9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#67,LCK 7#67,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27129:fsc|Experimental Factor: 7035:ssc|Experimental Factor: 522:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_67_mod.bam LCK_7_67.cram,bam cram,,,E MTAB 4617:LCK 7#67,0:125 1:125,A:211181074;C:167361986;G:152479010;T:214248000;N:87930,125,125,,,211181074,167361986,152479010,214248000,87930,ERX1497929,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.35381,0.35317,0.14449,0.14491,0.97865,0.97897,0.57854,0.58021,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4387,ERR1427396,ERX1497928,ERS1183230,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#66,SAMEA4012120,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012120|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#66|broker name:ArrayExpress|common name:zebrafish|fsc:23015|gfp:48|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#66|ssc:6562|tissue:Heart|well:B9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#66,LCK 7#66,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23015:fsc|Experimental Factor: 6562:ssc|Experimental Factor: 48:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_66_mod.bam LCK_7_66.cram,bam cram,,,E MTAB 4617:LCK 7#66,0:125 1:125,A:122494933;C:109921862;G:103257549;T:125665684;N:56722,125,125,,,122494933,109921862,103257549,125665684,56722,ERX1497928,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.18714,0.18418,0.0608,0.06082,0.9839,0.98441,0.60081,0.59623,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4388,ERR1427395,ERX1497927,ERS1183229,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#65,SAMEA4012119,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012119|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#65|broker name:ArrayExpress|common name:zebrafish|fsc:23857|gfp:308|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#65|ssc:4888|tissue:Heart|well:A9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#65,LCK 7#65,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23857:fsc|Experimental Factor: 4888:ssc|Experimental Factor: 308:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_65_mod.bam LCK_7_65.cram,bam cram,,,E MTAB 4617:LCK 7#65,0:125 1:125,A:96259909;C:89965165;G:84222055;T:99868995;N:43376,125,125,,,96259909,89965165,84222055,99868995,43376,ERX1497927,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.25582,0.25073,0.07651,0.07583,0.98044,0.98106,0.67809,0.67977,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4395,ERR1427388,ERX1497920,ERS1183222,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#59,SAMEA4012112,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012112|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#59|broker name:ArrayExpress|common name:zebrafish|fsc:20472|gfp:126|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#59|ssc:10300|tissue:Heart|well:C8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#59,LCK 7#59,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 20472:fsc|Experimental Factor: 10300:ssc|Experimental Factor: 126:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_59_mod.bam LCK_7_59.cram,bam cram,,,E MTAB 4617:LCK 7#59,0:125 1:125,A:134247255;C:121203898;G:112067297;T:140566781;N:62269,125,125,,,134247255,121203898,112067297,140566781,62269,ERX1497920,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.27548,0.27103,0.09818,0.09707,0.97861,0.97922,0.54371,0.57755,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4396,ERR1427387,ERX1497919,ERS1183221,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#58,SAMEA4012111,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012111|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#58|broker name:ArrayExpress|common name:zebrafish|fsc:30361|gfp:242|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#58|ssc:7886|tissue:Heart|well:B8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#58,LCK 7#58,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 30361:fsc|Experimental Factor: 7886:ssc|Experimental Factor: 242:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_58_mod.bam LCK_7_58.cram,bam cram,,,E MTAB 4617:LCK 7#58,0:125 1:125,A:165043952;C:161634321;G:152303735;T:174314970;N:75022,125,125,,,165043952,161634321,152303735,174314970,75022,ERX1497919,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.16408,0.16208,0.06572,0.06486,0.97918,0.97922,0.52752,0.52567,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4397,ERR1427386,ERX1497918,ERS1183220,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#57,SAMEA4012110,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012110|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#57|broker name:ArrayExpress|common name:zebrafish|fsc:30152|gfp:130|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#57|ssc:6428|tissue:Heart|well:A8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#57,LCK 7#57,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 30152:fsc|Experimental Factor: 6428:ssc|Experimental Factor: 130:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_57_mod.bam LCK_7_57.cram,bam cram,,,E MTAB 4617:LCK 7#57,0:125 1:125,A:81845074;C:82172065;G:76757417;T:87625766;N:38678,125,125,,,81845074,82172065,76757417,87625766,38678,ERX1497918,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.11381,0.11124,0.03217,0.03208,0.98253,0.98299,0.58282,0.58741,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4403,ERR1427380,ERX1497912,ERS1183214,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#51,SAMEA4012104,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012104|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#51|broker name:ArrayExpress|common name:zebrafish|fsc:28503|gfp:536|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#51|ssc:5896|tissue:Heart|well:C7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#51,LCK 7#51,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 28503:fsc|Experimental Factor: 5896:ssc|Experimental Factor: 536:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_51_mod.bam LCK_7_51.cram,bam cram,,,E MTAB 4617:LCK 7#51,0:125 1:125,A:68083321;C:57560520;G:49834107;T:71348826;N:28226,125,125,,,68083321,57560520,49834107,71348826,28226,ERX1497912,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.22734,0.22491,0.09383,0.09424,0.98019,0.98127,0.60101,0.59084,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4404,ERR1427379,ERX1497911,ERS1183213,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#50,SAMEA4012103,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012103|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#50|broker name:ArrayExpress|common name:zebrafish|fsc:27497|gfp:574|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#50|ssc:8308|tissue:Heart|well:B7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#50,LCK 7#50,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27497:fsc|Experimental Factor: 8308:ssc|Experimental Factor: 574:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_50_mod.bam LCK_7_50.cram,bam cram,,,E MTAB 4617:LCK 7#50,0:125 1:125,A:200436684;C:191639110;G:173623845;T:213497904;N:94207,125,125,,,200436684,191639110,173623845,213497904,94207,ERX1497911,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.08784,0.08742,0.04628,0.04599,0.98784,0.98823,0.5655,0.56486,125,125,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4406,ERR1427377,ERX1497909,ERS1183211,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#49,SAMEA4012101,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012101|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#49|broker name:ArrayExpress|common name:zebrafish|fsc:30443|gfp:456|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#49|ssc:8077|tissue:Heart|well:A7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#49,LCK 7#49,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 30443:fsc|Experimental Factor: 8077:ssc|Experimental Factor: 456:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_49_mod.bam LCK_7_49.cram,bam cram,,,E MTAB 4617:LCK 7#49,0:125 1:125,A:96840239;C:94376256;G:85197984;T:104185788;N:45483,125,125,,,96840239,94376256,85197984,104185788,45483,ERX1497909,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.17039,0.16705,0.05666,0.05595,0.98133,0.98196,0.59139,0.59279,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4412,ERR1427371,ERX1497903,ERS1183205,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#43,SAMEA4012095,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012095|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#43|broker name:ArrayExpress|common name:zebrafish|fsc:21270|gfp:120|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#43|ssc:7066|tissue:Heart|well:C6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#43,LCK 7#43,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 21270:fsc|Experimental Factor: 7066:ssc|Experimental Factor: 120:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_43_mod.bam LCK_7_43.cram,bam cram,,,E MTAB 4617:LCK 7#43,0:125 1:125,A:95132366;C:87995738;G:81475905;T:100137372;N:45119,125,125,,,95132366,87995738,81475905,100137372,45119,ERX1497903,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.21518,0.21129,0.06702,0.06612,0.97887,0.97944,0.5799,0.57556,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4413,ERR1427370,ERX1497902,ERS1183204,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#42,SAMEA4012094,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012094|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#42|broker name:ArrayExpress|common name:zebrafish|fsc:19274|gfp:88|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#42|ssc:6422|tissue:Heart|well:B6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#42,LCK 7#42,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 19274:fsc|Experimental Factor: 6422:ssc|Experimental Factor: 88:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_42_mod.bam LCK_7_42.cram,bam cram,,,E MTAB 4617:LCK 7#42,0:125 1:125,A:45015627;C:40505684;G:37787157;T:46787414;N:20618,125,125,,,45015627,40505684,37787157,46787414,20618,ERX1497902,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.14859,0.1471,0.0553,0.05579,0.98058,0.98151,0.57477,0.57968,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4414,ERR1427369,ERX1497901,ERS1183203,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#41,SAMEA4012093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012093|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#41|broker name:ArrayExpress|common name:zebrafish|fsc:20292|gfp:198|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#41|ssc:6233|tissue:Heart|well:A6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#41,LCK 7#41,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 20292:fsc|Experimental Factor: 6233:ssc|Experimental Factor: 198:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_41_mod.bam LCK_7_41.cram,bam cram,,,E MTAB 4617:LCK 7#41,0:125 1:125,A:89502636;C:89074499;G:83078909;T:95568395;N:39311,125,125,,,89502636,89074499,83078909,95568395,39311,ERX1497901,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.09383,0.09131,0.02199,0.02189,0.98569,0.98577,0.58856,0.59531,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4421,ERR1427362,ERX1497894,ERS1183196,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#35,SAMEA4012086,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012086|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#35|broker name:ArrayExpress|common name:zebrafish|fsc:26079|gfp:93|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#35|ssc:4930|tissue:Heart|well:C5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#35,LCK 7#35,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26079:fsc|Experimental Factor: 4930:ssc|Experimental Factor: 93:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_35_mod.bam LCK_7_35.cram,bam cram,,,E MTAB 4617:LCK 7#35,0:125 1:125,A:139844227;C:137312069;G:126169914;T:149207606;N:69934,125,125,,,139844227,137312069,126169914,149207606,69934,ERX1497894,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.19648,0.19308,0.05501,0.05463,0.98149,0.982,0.60289,0.60804,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4422,ERR1427361,ERX1497893,ERS1183195,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#34,SAMEA4012085,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012085|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#34|broker name:ArrayExpress|common name:zebrafish|fsc:25615|gfp:81|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#34|ssc:5934|tissue:Heart|well:B5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#34,LCK 7#34,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25615:fsc|Experimental Factor: 5934:ssc|Experimental Factor: 81:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_34_mod.bam LCK_7_34.cram,bam cram,,,E MTAB 4617:LCK 7#34,0:125 1:125,A:134481938;C:127574886;G:118538403;T:142102568;N:61455,125,125,,,134481938,127574886,118538403,142102568,61455,ERX1497893,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.19982,0.1964,0.06657,0.0662,0.98092,0.98119,0.59089,0.58445,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4423,ERR1427360,ERX1497892,ERS1183194,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#33,SAMEA4012084,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012084|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#33|broker name:ArrayExpress|common name:zebrafish|fsc:28221|gfp:414|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#33|ssc:5341|tissue:Heart|well:A5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#33,LCK 7#33,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 28221:fsc|Experimental Factor: 5341:ssc|Experimental Factor: 414:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_33_mod.bam LCK_7_33.cram,bam cram,,,E MTAB 4617:LCK 7#33,0:125 1:125,A:93220735;C:94390552;G:86770054;T:100705096;N:43313,125,125,,,93220735,94390552,86770054,100705096,43313,ERX1497892,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.09686,0.09522,0.02902,0.02873,0.98228,0.98279,0.54935,0.54646,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4427,ERR1427356,ERX1497888,ERS1183190,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#3,SAMEA4012080,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012080|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#3|broker name:ArrayExpress|common name:zebrafish|fsc:25075|gfp:108|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#3|ssc:7682|tissue:Heart|well:C1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#3,LCK 7#3,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25075:fsc|Experimental Factor: 7682:ssc|Experimental Factor: 108:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_3_mod.bam LCK_7_3.cram,bam cram,,,E MTAB 4617:LCK 7#3,0:125 1:125,A:58493174;C:54183075;G:50060440;T:61036959;N:28352,125,125,,,58493174,54183075,50060440,61036959,28352,ERX1497888,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.15762,0.1526,0.04924,0.04785,0.97906,0.97966,0.55641,0.55037,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4430,ERR1427353,ERX1497885,ERS1183187,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#27,SAMEA4012077,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012077|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#27|broker name:ArrayExpress|common name:zebrafish|fsc:29359|gfp:456|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#27|ssc:10950|tissue:Heart|well:C4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#27,LCK 7#27,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 29359:fsc|Experimental Factor: 10950:ssc|Experimental Factor: 456:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_27_mod.bam LCK_7_27.cram,bam cram,,,E MTAB 4617:LCK 7#27,0:125 1:125,A:116175271;C:110956295;G:101584573;T:123371066;N:51045,125,125,,,116175271,110956295,101584573,123371066,51045,ERX1497885,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.25865,0.25265,0.08041,0.07902,0.97601,0.97595,0.55457,0.55357,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4431,ERR1427352,ERX1497884,ERS1183186,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#26,SAMEA4012076,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012076|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#26|broker name:ArrayExpress|common name:zebrafish|fsc:25525|gfp:162|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#26|ssc:5861|tissue:Heart|well:B4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#26,LCK 7#26,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25525:fsc|Experimental Factor: 5861:ssc|Experimental Factor: 162:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_26_mod.bam LCK_7_26.cram,bam cram,,,E MTAB 4617:LCK 7#26,0:125 1:125,A:84022783;C:79751329;G:73366671;T:88820379;N:40588,125,125,,,84022783,79751329,73366671,88820379,40588,ERX1497884,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.13334,0.13062,0.04098,0.04053,0.98405,0.98439,0.43923,0.56542,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4432,ERR1427351,ERX1497883,ERS1183185,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#25,SAMEA4012075,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012075|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#25|broker name:ArrayExpress|common name:zebrafish|fsc:28284|gfp:515|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#25|ssc:8791|tissue:Heart|well:A4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#25,LCK 7#25,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 28284:fsc|Experimental Factor: 8791:ssc|Experimental Factor: 515:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_25_mod.bam LCK_7_25.cram,bam cram,,,E MTAB 4617:LCK 7#25,0:125 1:125,A:93291373;C:90572911;G:83617400;T:99965116;N:42450,125,125,,,93291373,90572911,83617400,99965116,42450,ERX1497883,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.22059,0.21595,0.06285,0.06239,0.97739,0.97755,0.60441,0.5941,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4438,ERR1427345,ERX1497877,ERS1183179,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#2,SAMEA4012069,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012069|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#2|broker name:ArrayExpress|common name:zebrafish|fsc:26546|gfp:74|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#2|ssc:5884|tissue:Heart|well:B1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#2,LCK 7#2,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26546:fsc|Experimental Factor: 5884:ssc|Experimental Factor: 74:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_2_mod.bam LCK_7_2.cram,bam cram,,,E MTAB 4617:LCK 7#2,0:125 1:125,A:50810642;C:45505266;G:42437381;T:52252338;N:22373,125,125,,,50810642,45505266,42437381,52252338,22373,ERX1497877,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.13878,0.13634,0.03454,0.03422,0.98179,0.98238,0.53282,0.54119,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4439,ERR1427344,ERX1497876,ERS1183178,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#19,SAMEA4012068,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012068|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#19|broker name:ArrayExpress|common name:zebrafish|fsc:27939|gfp:269|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#19|ssc:7748|tissue:Heart|well:C3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#19,LCK 7#19,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27939:fsc|Experimental Factor: 7748:ssc|Experimental Factor: 269:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_19_mod.bam LCK_7_19.cram,bam cram,,,E MTAB 4617:LCK 7#19,0:125 1:125,A:123448577;C:117648440;G:109679332;T:127799152;N:59249,125,125,,,123448577,117648440,109679332,127799152,59249,ERX1497876,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.20997,0.20449,0.04702,0.04606,0.98013,0.98068,0.58105,0.58018,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4440,ERR1427343,ERX1497875,ERS1183177,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#18,SAMEA4012067,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012067|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#18|broker name:ArrayExpress|common name:zebrafish|fsc:23930|gfp:89|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#18|ssc:7002|tissue:Heart|well:B3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#18,LCK 7#18,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23930:fsc|Experimental Factor: 7002:ssc|Experimental Factor: 89:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_18_mod.bam LCK_7_18.cram,bam cram,,,E MTAB 4617:LCK 7#18,0:125 1:125,A:116722795;C:108761302;G:102297772;T:120311653;N:53978,125,125,,,116722795,108761302,102297772,120311653,53978,ERX1497875,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.17035,0.16607,0.04165,0.04071,0.98275,0.98315,0.57334,0.56296,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4441,ERR1427342,ERX1497874,ERS1183176,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#17,SAMEA4012066,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012066|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#17|broker name:ArrayExpress|common name:zebrafish|fsc:19157|gfp:158|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#17|ssc:7404|tissue:Heart|well:A3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#17,LCK 7#17,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 19157:fsc|Experimental Factor: 7404:ssc|Experimental Factor: 158:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_17_mod.bam LCK_7_17.cram,bam cram,,,E MTAB 4617:LCK 7#17,0:125 1:125,A:114273839;C:106761242;G:100217178;T:118680369;N:52122,125,125,,,114273839,106761242,100217178,118680369,52122,ERX1497874,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.26249,0.25596,0.06917,0.06842,0.9737,0.97425,0.59255,0.59411,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4447,ERR1427336,ERX1497868,ERS1183170,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#11,SAMEA4012060,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012060|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#11|broker name:ArrayExpress|common name:zebrafish|fsc:23053|gfp:148|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#11|ssc:3985|tissue:Heart|well:C2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#11,LCK 7#11,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23053:fsc|Experimental Factor: 3985:ssc|Experimental Factor: 148:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_11_mod.bam LCK_7_11.cram,bam cram,,,E MTAB 4617:LCK 7#11,0:125 1:125,A:94603298;C:90252097;G:83046109;T:99899414;N:44332,125,125,,,94603298,90252097,83046109,99899414,44332,ERX1497868,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.24988,0.24291,0.07669,0.07453,0.97857,0.97901,0.52877,0.53451,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4448,ERR1427335,ERX1497867,ERS1183169,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#10,SAMEA4012059,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012059|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#10|broker name:ArrayExpress|common name:zebrafish|fsc:26350|gfp:91|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#10|ssc:5717|tissue:Heart|well:B2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#10,LCK 7#10,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26350:fsc|Experimental Factor: 5717:ssc|Experimental Factor: 91:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_10_mod.bam LCK_7_10.cram,bam cram,,,E MTAB 4617:LCK 7#10,0:125 1:125,A:136048498;C:130651014;G:121379521;T:142822578;N:64889,125,125,,,136048498,130651014,121379521,142822578,64889,ERX1497867,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.14978,0.14551,0.04586,0.0445,0.98516,0.98559,0.55716,0.54592,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4449,ERR1427334,ERX1497866,ERS1183168,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#1,SAMEA4012058,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012058|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#1|broker name:ArrayExpress|common name:zebrafish|fsc:22006|gfp:487|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#1|ssc:6542|tissue:Heart|well:A1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#1,LCK 7#1,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 22006:fsc|Experimental Factor: 6542:ssc|Experimental Factor: 487:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_1_mod.bam LCK_7_1.cram,bam cram,,,E MTAB 4617:LCK 7#1,0:125 1:125,A:128250593;C:122748202;G:114418508;T:135400263;N:59934,125,125,,,128250593,122748202,114418508,135400263,59934,ERX1497866,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.15168,0.14994,0.07129,0.07092,0.98202,0.98163,0.61662,0.63065,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
8065,ERR035546,ERX013539,ERS017860,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult heart,SAMEA782570,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460 part2:5625 2,ZFheart 2 RNA 1523493,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented  LiCl precipitated  reverse transcribed with random primers  a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.,Experimental Factor: ORGANISM PART:heart,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16,5625_2.srf,srf,4268641920.0,26679012.0,E MTAB 460 part2:5625 2.srf,0:76 1:8 2:76,A:1091431814;C:927546313;G:930574449;T:1098343870;N:7313378,76,8,76,,1091431814,927546313,930574449,1098343870,7313378,ERX013539,ERS017860,ERA033503,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.89019,0.88267,0.09729,0.09648,0.75396,0.75682,0.49617,0.48086,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Heart,Cardiovascular System
8071,ERR023150,ERX009447,ERS017860,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult heart,SAMEA782570,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460:4191 7,RNA from Zebrafish adult heart,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Experimental Factor: ORGANISM PART:heart,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16,4191_7.srf,srf,3679011648.0,24204024.0,E MTAB 460:4191 7.srf,0:76 1:76,A:1284614952;C:552903359;G:563080702;T:1273094378;N:5318257,76,76,,,1284614952,552903359,563080702,1273094378,5318257,ERX009447,ERS017860,ERA015648,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.85359,0.84739,0.30719,0.3063,0.82806,0.82686,0.52003,0.52279,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Heart,Cardiovascular System
8073,ERR023145,ERX009445,ERS017860,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Zebrafish adult heart,SAMEA782570,Wellcome Sanger Institute,ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782570|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult heart|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:heart|sample name:E MTAB 460:Zebrafish adult heart|sex:mixed,,,,,,,,,Sanger zebrafish sequencing,E MTAB 460:3212 7,RNA from Zebrafish adult heart,Sanger zebrafish sequencing,Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.,Experimental Factor: ORGANISM PART:heart,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000447,Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing,ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16,3212_7.srf,srf,590858656.0,3887228.0,E MTAB 460:3212 7.srf,0:76 1:76,A:198026008;C:95340719;G:91816629;T:200078264;N:5597036,76,76,,,198026008,95340719,91816629,200078264,5597036,ERX009445,ERS017860,ERA015648,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.85463,0.85526,0.2737,0.27538,0.82189,0.82282,0.55114,0.5482,76,76,B,B,biological fallback assumption,illumina,early_illumina,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2011-02-03,Adult,Adult,Heart,Cardiovascular System
10216,ERR6501834,ERX6129007,ERS7415871,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 3,SAMEA9691614,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691614|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 6 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 3|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 3 p,Uninjured 3 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz,fastq fastq,18723567013.0,65061888.0,E MTAB 10860:un 3 R,0:143.87 1:143.91,A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225,143,143,,,4417527025,4932613578,4960694819,4412305366,426225,ERX6129007,ERS7415871,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96755,0.96744,0.18873,0.18936,0.72868,0.73235,0.632,0.6437,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10217,ERR6501833,ERX6129006,ERS7415870,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 2,SAMEA9691613,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691613|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 5 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 2|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 2 p,Uninjured 2 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz,fastq fastq,16871358399.0,59064661.0,E MTAB 10860:un 2 R,0:142.77 1:142.88,A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056,142,142,,,4041490134,4380856328,4414614946,4033723935,673056,ERX6129006,ERS7415870,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96589,0.9656,0.15519,0.15447,0.70887,0.71062,0.60267,0.60735,150,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10218,ERR6501832,ERX6129005,ERS7415869,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 1,SAMEA9691612,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691612|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 4 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 1|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 1 p,Uninjured 1 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz,fastq fastq,22029484310.0,76938931.0,E MTAB 10860:un 1 R,0:143.11 1:143.22,A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752,143,143,,,5407867825,5589867496,5636111894,5394805343,831752,ERX6129005,ERS7415869,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.9602,0.95957,0.14282,0.14408,0.69649,0.69954,0.56712,0.56916,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10219,ERR6501831,ERX6129004,ERS7415868,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 3,SAMEA9691611,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691611|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 3 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 3|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 3 p,Injured 3 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz,fastq fastq,7393087749.0,25640713.0,E MTAB 10860:in 3 R,0:144.14 1:144.20,A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175,144,144,,,1776335117,1913125420,1928181998,1775255039,190175,ERX6129004,ERS7415868,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96032,0.96001,0.15921,0.15882,0.71417,0.71869,0.59876,0.595,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10220,ERR6501830,ERX6129003,ERS7415867,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 2,SAMEA9691610,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691610|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 2 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 2|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 2 p,Injured 2 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz,fastq fastq,9437508186.0,33059234.0,E MTAB 10860:in 2 R,0:142.70 1:142.77,A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351,142,142,,,2291798254,2421252733,2436117818,2288107030,232351,ERX6129003,ERS7415867,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96099,0.96042,0.14616,0.14802,0.70331,0.70674,0.53288,0.54459,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10221,ERR6501829,ERX6129002,ERS7415866,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 1,SAMEA9691609,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691609|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 1 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 1|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 1 p,Injured 1 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz,fastq fastq,15465552702.0,54194727.0,E MTAB 10860:in 1 R,0:142.59 1:142.78,A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648,142,142,,,3807777989,3911855097,3946385823,3798685145,848648,ERX6129002,ERS7415866,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.95721,0.95688,0.14331,0.14374,0.70262,0.70445,0.5114,0.52855,140,140,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
11174,ERR10180601,ERX9716167,ERS13447543,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens WT 2,SAMEA111349996,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349996|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens WT 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:lens|sample name:E MTAB 12172:lens WT 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens WT 2 p,lens WT 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-2-CCATCCGC-AAGGCGTA_S01_L005_R1_001.fastq.gz 5089-PP-2-CCATCCGC-AAGGCGTA_S01_L005_R2_001.fastq.gz,fastq fastq,16333543200.0,54445144.0,E MTAB 12172:5089 PP 2 CCATCCGC AAGGCGTA S01 L005 R,0:150 1:150,A:4190619330;C:3994540430;G:4078805527;T:4069157225;N:420688,150,150,,,4190619330,3994540430,4078805527,4069157225,420688,ERX9716167,ERS13447543,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.93689,0.9406,0.04209,0.04067,0.82698,0.82666,0.36086,0.43109,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11175,ERR10180600,ERX9716166,ERS13447542,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens WT 1,SAMEA111349995,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349995|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens WT 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:lens|sample name:E MTAB 12172:lens WT 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens WT 1 p,lens WT 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-1-ACAAGGCA-TCGCGCAA_S01_L005_R1_001.fastq.gz 5089-PP-1-ACAAGGCA-TCGCGCAA_S01_L005_R2_001.fastq.gz,fastq fastq,15407010900.0,51356703.0,E MTAB 12172:5089 PP 1 ACAAGGCA TCGCGCAA S01 L005 R,0:150 1:150,A:3964097798;C:3754084768;G:3842793010;T:3845637263;N:398061,150,150,,,3964097798,3754084768,3842793010,3845637263,398061,ERX9716166,ERS13447542,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.94811,0.95125,0.04583,0.044,0.81844,0.81836,0.35718,0.43545,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11176,ERR10180599,ERX9716165,ERS13447541,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens nrf2 mut 2,SAMEA111349994,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349994|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens nrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:lens|sample name:E MTAB 12172:lens nrf2 mut 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens nrf2 mut 2 p,lens nrf2 mut 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:nrf2 mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-6-ACCAACAG-GTTTGCTC_S01_L005_R1_001.fastq.gz 5089-PP-6-ACCAACAG-GTTTGCTC_S01_L005_R2_001.fastq.gz,fastq fastq,16160592300.0,53868641.0,E MTAB 12172:5089 PP 6 ACCAACAG GTTTGCTC S01 L005 R,0:150 1:150,A:4169968181;C:3949888212;G:4033930705;T:4006382078;N:423124,150,150,,,4169968181,3949888212,4033930705,4006382078,423124,ERX9716165,ERS13447541,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.96029,0.95994,0.04416,0.04259,0.82035,0.81982,0.36027,0.36601,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11177,ERR10180598,ERX9716164,ERS13447540,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens nrf2 mut 1,SAMEA111349993,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349993|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens nrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:lens|sample name:E MTAB 12172:lens nrf2 mut 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens nrf2 mut 1 p,lens nrf2 mut 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:nrf2 mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-5-GCACACAA-CTTGACGA_S01_L005_R1_001.fastq.gz 5089-PP-5-GCACACAA-CTTGACGA_S01_L005_R2_001.fastq.gz,fastq fastq,13265052900.0,44216843.0,E MTAB 12172:5089 PP 5 GCACACAA CTTGACGA S01 L005 R,0:150 1:150,A:3416009346;C:3243776635;G:3305220346;T:3299701557;N:345016,150,150,,,3416009346,3243776635,3305220346,3299701557,345016,ERX9716164,ERS13447540,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.96137,0.95958,0.04396,0.04235,0.81505,0.8156,0.42582,0.44063,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11178,ERR10180597,ERX9716163,ERS13447539,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens abanrf2 mut 2,SAMEA111349992,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349992|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abanrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:lens|sample name:E MTAB 12172:lens abanrf2 mut 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens abanrf2 mut 2 p,lens abanrf2 mut 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout; nrf2 double mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-8-AACACCAC-GGTGTGAG_S01_L005_R1_001.fastq.gz 5089-PP-8-AACACCAC-GGTGTGAG_S01_L005_R2_001.fastq.gz,fastq fastq,15388634400.0,51295448.0,E MTAB 12172:5089 PP 8 AACACCAC GGTGTGAG S01 L005 R,0:150 1:150,A:3958631492;C:3788327811;G:3838374812;T:3802892334;N:407951,150,150,,,3958631492,3788327811,3838374812,3802892334,407951,ERX9716163,ERS13447539,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.95795,0.95848,0.03631,0.0352,0.82686,0.82702,0.44398,0.43981,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11179,ERR10180596,ERX9716162,ERS13447538,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens abanrf2 mut 1,SAMEA111349991,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349991|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abanrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:lens|sample name:E MTAB 12172:lens abanrf2 mut 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens abanrf2 mut 1 p,lens abanrf2 mut 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout; nrf2 double mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-7-ATGTTCCT-TCAGCGCC_S01_L005_R1_001.fastq.gz 5089-PP-7-ATGTTCCT-TCAGCGCC_S01_L005_R2_001.fastq.gz,fastq fastq,15994173600.0,53313912.0,E MTAB 12172:5089 PP 7 ATGTTCCT TCAGCGCC S01 L005 R,0:150 1:150,A:4099988245;C:3917478063;G:3992545834;T:3983743906;N:417552,150,150,,,4099988245,3917478063,3992545834,3983743906,417552,ERX9716162,ERS13447538,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.96127,0.95941,0.04117,0.03964,0.82047,0.82057,0.38606,0.37713,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11180,ERR10180595,ERX9716161,ERS13447537,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens abaKO 2,SAMEA111349990,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349990|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abaKO 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:lens|sample name:E MTAB 12172:lens abaKO 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens abaKO 2 p,lens abaKO 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-4-TCGCGCAA-ACAAGGCA_S01_L005_R1_001.fastq.gz 5089-PP-4-TCGCGCAA-ACAAGGCA_S01_L005_R2_001.fastq.gz,fastq fastq,17799042900.0,59330143.0,E MTAB 12172:5089 PP 4 TCGCGCAA ACAAGGCA S01 L005 R,0:150 1:150,A:4545266681;C:4379648812;G:4457651334;T:4416025472;N:450601,150,150,,,4545266681,4379648812,4457651334,4416025472,450601,ERX9716161,ERS13447537,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.8747,0.87804,0.03407,0.03304,0.83999,0.84047,0.41026,0.42746,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11181,ERR10180594,ERX9716160,ERS13447536,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,lens abaKO 1,SAMEA111349989,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349989|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:lens abaKO 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:lens|sample name:E MTAB 12172:lens abaKO 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:lens abaKO 1 p,lens abaKO 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R1_001.fastq.gz 5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R2_001.fastq.gz,fastq fastq,18850381500.0,62834605.0,E MTAB 12172:5089 PP 3 AAGGCGTA CCATCCGC S01 L005 R,0:150 1:150,A:4831021904;C:4613611754;G:4712103573;T:4693153324;N:490945,150,150,,,4831021904,4613611754,4712103573,4693153324,490945,ERX9716160,ERS13447536,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.94079,0.94389,0.04169,0.04008,0.82367,0.82524,0.4379,0.43771,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11182,ERR10180593,ERX9716159,ERS13447535,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart WT 2,SAMEA111349988,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349988|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart WT 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 12172:heart WT 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart WT 2 p,heart WT 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-2-GATATGAA-TACGGCAG_S1_L001_R1_001.fastq.gz 5539-JP-2-GATATGAA-TACGGCAG_S1_L001_R2_001.fastq.gz,fastq fastq,14304623100.0,47682077.0,E MTAB 12172:5539 JP 2 GATATGAA TACGGCAG S1 L001 R,0:150 1:150,A:3881337642;C:3260590900;G:3395614407;T:3766879544;N:200607,150,150,,,3881337642,3260590900,3395614407,3766879544,200607,ERX9716159,ERS13447535,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.94254,0.94698,0.05301,0.05137,0.77502,0.77352,0.50073,0.50274,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11183,ERR10180592,ERX9716158,ERS13447534,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart WT 1,SAMEA111349987,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349987|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart WT 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 12172:heart WT 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart WT 1 p,heart WT 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-1-GTCCGATC-GCCAATCC_S1_L001_R1_001.fastq.gz 5539-JP-1-GTCCGATC-GCCAATCC_S1_L001_R2_001.fastq.gz,fastq fastq,19185453300.0,63951511.0,E MTAB 12172:5539 JP 1 GTCCGATC GCCAATCC S1 L001 R,0:150 1:150,A:5172411335;C:4401564793;G:4571457514;T:5039775881;N:243777,150,150,,,5172411335,4401564793,4571457514,5039775881,243777,ERX9716158,ERS13447534,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.94765,0.95188,0.0548,0.05291,0.75986,0.76015,0.49801,0.49914,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11184,ERR10180591,ERX9716157,ERS13447533,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart nrf2 mut 2,SAMEA111349986,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349986|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart nrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:heart|sample name:E MTAB 12172:heart nrf2 mut 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart nrf2 mut 2 p,heart nrf2 mut 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:nrf2 mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-6-CCTTTCAC-TCTTGTTT_S1_L001_R1_001.fastq.gz 5539-JP-6-CCTTTCAC-TCTTGTTT_S1_L001_R2_001.fastq.gz,fastq fastq,15506772300.0,51689241.0,E MTAB 12172:5539 JP 6 CCTTTCAC TCTTGTTT S1 L001 R,0:150 1:150,A:4206068868;C:3553449100;G:3659363790;T:4087684595;N:205947,150,150,,,4206068868,3553449100,3659363790,4087684595,205947,ERX9716157,ERS13447533,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.94875,0.95145,0.05898,0.05611,0.77254,0.77293,0.43478,0.41873,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11185,ERR10180590,ERX9716156,ERS13447532,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart nrf2 mut 1,SAMEA111349985,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349985|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart nrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:nrf2 mutant|organism part:heart|sample name:E MTAB 12172:heart nrf2 mut 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart nrf2 mut 1 p,heart nrf2 mut 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:nrf2 mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-5-CACTAGAC-TGAGGACT_S1_L001_R1_001.fastq.gz 5539-JP-5-CACTAGAC-TGAGGACT_S1_L001_R2_001.fastq.gz,fastq fastq,21738824700.0,72462749.0,E MTAB 12172:5539 JP 5 CACTAGAC TGAGGACT S1 L001 R,0:150 1:150,A:5871744282;C:5014617409;G:5151654454;T:5700519276;N:289279,150,150,,,5871744282,5014617409,5151654454,5700519276,289279,ERX9716156,ERS13447532,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.95074,0.95283,0.05595,0.05426,0.77193,0.77163,0.43329,0.49376,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11186,ERR10180589,ERX9716155,ERS13447531,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart abanrf2 mut 2,SAMEA111349984,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349984|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abanrf2 mut 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:heart|sample name:E MTAB 12172:heart abanrf2 mut 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart abanrf2 mut 2 p,heart abanrf2 mut 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout; nrf2 double mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-8-TACGGCAG-GATATGAA_S1_L001_R1_001.fastq.gz 5539-JP-8-TACGGCAG-GATATGAA_S1_L001_R2_001.fastq.gz,fastq fastq,17223550800.0,57411836.0,E MTAB 12172:5539 JP 8 TACGGCAG GATATGAA S1 L001 R,0:150 1:150,A:4719158105;C:3846804288;G:4048574589;T:4608706331;N:307487,150,150,,,4719158105,3846804288,4048574589,4608706331,307487,ERX9716155,ERS13447531,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.93762,0.93789,0.0641,0.05916,0.77171,0.77465,0.50708,0.52073,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11187,ERR10180588,ERX9716154,ERS13447530,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart abanrf2 mut 1,SAMEA111349983,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349983|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abanrf2 mut 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout; nrf2 double mutant|organism part:heart|sample name:E MTAB 12172:heart abanrf2 mut 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart abanrf2 mut 1 p,heart abanrf2 mut 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout; nrf2 double mutant,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-7-GCCAATCC-GTCCGATC_S1_L001_R1_001.fastq.gz 5539-JP-7-GCCAATCC-GTCCGATC_S1_L001_R2_001.fastq.gz,fastq fastq,14585545800.0,48618486.0,E MTAB 12172:5539 JP 7 GCCAATCC GTCCGATC S1 L001 R,0:150 1:150,A:3991503126;C:3300292702;G:3398962745;T:3894599059;N:188168,150,150,,,3991503126,3300292702,3398962745,3894599059,188168,ERX9716154,ERS13447530,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.9375,0.94022,0.06736,0.06462,0.76445,0.76495,0.50218,0.51223,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11188,ERR10180587,ERX9716153,ERS13447529,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart abaKO 2,SAMEA111349982,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349982|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abaKO 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:heart|sample name:E MTAB 12172:heart abaKO 2|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart abaKO 2 p,heart abaKO 2 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-4-TGTGTCAG-CACCTGTA_S1_L001_R1_001.fastq.gz 5539-JP-4-TGTGTCAG-CACCTGTA_S1_L001_R2_001.fastq.gz,fastq fastq,16499634000.0,54998780.0,E MTAB 12172:5539 JP 4 TGTGTCAG CACCTGTA S1 L001 R,0:150 1:150,A:4448248023;C:3776948921;G:3924285767;T:4349924059;N:227230,150,150,,,4448248023,3776948921,3924285767,4349924059,227230,ERX9716153,ERS13447529,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.92566,0.92887,0.05292,0.05145,0.76741,0.76759,0.44001,0.44327,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
11189,ERR10180586,ERX9716152,ERS13447528,ERP140949,PRJEB56027,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E-MTAB-12172,Transcriptome Analysis,To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency  we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT  cryaba /   nrf2fh318/fh318  and cryaba / ;nrf2fh318/fh318 lines.,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,,Protocols: adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.,heart abaKO 1,SAMEA111349981,Vanderbilt Univiersity,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24|External Id:SAMEA111349981|INSDC center alias:Vanderbilt Univiersity|INSDC center name:Vanderbilt Univiersity|INSDC first public:2022 09 24T00:21:08Z|INSDC last update:2022 09 24T00:21:08Z|INSDC status:public|Submitter Id:E MTAB 12172:heart abaKO 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:cryaba knockout|organism part:heart|sample name:E MTAB 12172:heart abaKO 1|sex:male,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,E MTAB 12172:heart abaKO 1 p,heart abaKO 1 p,Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,adult zebrafish heart tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta  T. and M.C. Mullins  Dissection of organs from the adult zebrafish. J Vis Exp  201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction.  Raw sequencing reads were obtained for the paired end samples.,Experimental Factor: genotype:cryaba knockout,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140949,Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress,ENA FIRST PUBLIC:2022 09 24|ENA LAST UPDATE:2022 09 24,5539-JP-3-AGTCAGGT-GTAACCAC_S1_L001_R1_001.fastq.gz 5539-JP-3-AGTCAGGT-GTAACCAC_S1_L001_R2_001.fastq.gz,fastq fastq,23723109000.0,79077030.0,E MTAB 12172:5539 JP 3 AGTCAGGT GTAACCAC S1 L001 R,0:150 1:150,A:6432327752;C:5406026214;G:5617874748;T:6266589522;N:290764,150,150,,,6432327752,5406026214,5617874748,6266589522,290764,ERX9716152,ERS13447528,ERA17903080,Vanderbilt Univiersity|European Nucleotide Archive,Vanderbilt Univiersity|European Nucleotide Archive,2,0.94728,0.95029,0.05332,0.05201,0.76646,0.76838,0.50604,0.50579,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-09-24,Adult,Adult,Heart,Cardiovascular System
15017,ERR12352459,ERX11729321,ERS17282126,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Trpc6a KO sham 3,SAMEA114857167,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857167|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Trpc6a KO sham 3 p,Trpc6a KO sham 3 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,3-Trpc6-KO-sham_R1_001.fastq.gz 3-Trpc6-KO-sham_R2_001.fastq.gz,fastq fastq,9486677705.0,33558571.0,E MTAB 13603:3 Trpc6 KO sham R,0:141.09 1:141.60,A:2537673665;C:2192877777;G:2224713939;T:2525303945;N:6108379,141,141,,,2537673665,2192877777,2224713939,2525303945,6108379,ERX11729321,ERS17282126,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95729,0.95618,0.07289,0.07124,0.7725,0.77481,0.52646,0.53221,149,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15018,ERR12352449,ERX11729311,ERS17282116,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Control 7dpa 1,SAMEA114857157,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857157|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Control 7dpa 1 p,Control 7dpa 1 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,4-Control-7dpa_R2_001.fastq.gz 4-Control-7dpa_R1_001.fastq.gz,fastq fastq,6795430724.0,23938740.0,E MTAB 13603:4 Control 7dpa R,0:141.55 1:142.32,A:1815845541;C:1567718020;G:1597570908;T:1808008628;N:6287627,141,142,,,1815845541,1567718020,1597570908,1808008628,6287627,ERX11729311,ERS17282116,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94648,0.94563,0.09062,0.08917,0.75087,0.75333,0.52273,0.51959,149,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15019,ERR12352452,ERX11729314,ERS17282119,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Control sham 1,SAMEA114857160,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857160|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Control sham 1 p,Control sham 1 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,1-Control-sham_R1_001.fastq.gz 1-Control-sham_R2_001.fastq.gz,fastq fastq,15636676800.0,52122256.0,E MTAB 13603:1 Control sham R,0:150 1:150,A:4263031098;C:3519985187;G:3706349796;T:4147090133;N:220586,150,150,,,4263031098,3519985187,3706349796,4147090133,220586,ERX11729314,ERS17282119,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94648,0.94897,0.06005,0.05942,0.76712,0.76822,0.51256,0.50643,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15020,ERR12352451,ERX11729313,ERS17282118,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Control 7dpa 3,SAMEA114857159,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857159|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Control 7dpa 3 p,Control 7dpa 3 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,6-Control-7dpa_R1_001.fastq.gz 6-Control-7dpa_R2_001.fastq.gz,fastq fastq,8220300600.0,27401002.0,E MTAB 13603:6 Control 7dpa R,0:150 1:150,A:2242736911;C:1858506669;G:1911004513;T:2207938253;N:114254,150,150,,,2242736911,1858506669,1911004513,2207938253,114254,ERX11729313,ERS17282118,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94374,0.94281,0.07308,0.07247,0.74028,0.7418,0.50319,0.50503,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15021,ERR12352457,ERX11729319,ERS17282124,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Trpc6a KO sham 1,SAMEA114857165,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857165|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Trpc6a KO sham 1 p,Trpc6a KO sham 1 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,1-Trpc6-KO-sham_R1_001.fastq.gz 1-Trpc6-KO-sham_R2_001.fastq.gz,fastq fastq,16463891400.0,54879638.0,E MTAB 13603:1 Trpc6 KO sham R,0:150 1:150,A:4481016793;C:3727761629;G:3905685351;T:4349193797;N:233830,150,150,,,4481016793,3727761629,3905685351,4349193797,233830,ERX11729319,ERS17282124,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95234,0.95051,0.05908,0.05789,0.77477,0.77605,0.49876,0.50128,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15022,ERR12352458,ERX11729320,ERS17282125,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Trpc6a KO sham 2,SAMEA114857166,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857166|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO sham 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO sham 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Trpc6a KO sham 2 p,Trpc6a KO sham 2 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,2-Trpc6-KO-sham_R1_001.fastq.gz 2-Trpc6-KO-sham_R2_001.fastq.gz,fastq fastq,10449824700.0,34832749.0,E MTAB 13603:2 Trpc6 KO sham R,0:150 1:150,A:2842222574;C:2368784549;G:2449245548;T:2789428695;N:143334,150,150,,,2842222574,2368784549,2449245548,2789428695,143334,ERX11729320,ERS17282125,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.9539,0.95284,0.05851,0.05781,0.77425,0.77656,0.50514,0.50462,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15023,ERR12352453,ERX11729315,ERS17282120,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Control sham 2,SAMEA114857161,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857161|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control sham 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:sham operated|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control sham 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Control sham 2 p,Control sham 2 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,2-Control-sham_R1_001.fastq.gz 2-Control-sham_R2_001.fastq.gz,fastq fastq,13714149300.0,45713831.0,E MTAB 13603:2 Control sham R,0:150 1:150,A:3744799859;C:3102314317;G:3246683965;T:3620157056;N:194103,150,150,,,3744799859,3102314317,3246683965,3620157056,194103,ERX11729315,ERS17282120,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94672,0.94688,0.05944,0.05917,0.76654,0.76773,0.51792,0.51959,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15024,ERR12352450,ERX11729312,ERS17282117,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Control 7dpa 2,SAMEA114857158,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857158|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Control 7dpa 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Control 7dpa 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Control 7dpa 2 p,Control 7dpa 2 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,5-Control-7dpa_R1_001.fastq.gz 5-Control-7dpa_R2_001.fastq.gz,fastq fastq,9830629200.0,32768764.0,E MTAB 13603:5 Control 7dpa R,0:150 1:150,A:2655376287;C:2237942590;G:2372252275;T:2564920802;N:137246,150,150,,,2655376287,2237942590,2372252275,2564920802,137246,ERX11729312,ERS17282117,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94476,0.94389,0.06625,0.06506,0.74197,0.7441,0.50589,0.50685,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15025,ERR12352454,ERX11729316,ERS17282121,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Trpc6a KO 7dpa 1,SAMEA114857162,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857162|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 1|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 1|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Trpc6a KO 7dpa 1 p,Trpc6a KO 7dpa 1 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,4-Trpc6-KO-7dpa_R2_001.fastq.gz 4-Trpc6-KO-7dpa_R1_001.fastq.gz,fastq fastq,5379338700.0,17931129.0,E MTAB 13603:4 Trpc6 KO 7dpa R,0:150 1:150,A:1451310854;C:1236467303;G:1283161720;T:1408322640;N:76183,150,150,,,1451310854,1236467303,1283161720,1408322640,76183,ERX11729316,ERS17282121,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94369,0.94789,0.06027,0.06036,0.74647,0.74649,0.4767,0.50107,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15026,ERR12352455,ERX11729317,ERS17282122,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Trpc6a KO 7dpa 2,SAMEA114857163,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857163|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 2|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 2|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Trpc6a KO 7dpa 2 p,Trpc6a KO 7dpa 2 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,5-Trpc6-KO-7dpa_R2_001.fastq.gz 5-Trpc6-KO-7dpa_R1_001.fastq.gz,fastq fastq,14033980200.0,46779934.0,E MTAB 13603:5 Trpc6 KO 7dpa R,0:150 1:150,A:3810908166;C:3197374649;G:3343702230;T:3681798453;N:196702,150,150,,,3810908166,3197374649,3343702230,3681798453,196702,ERX11729317,ERS17282122,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.94801,0.94661,0.06342,0.06201,0.74834,0.75207,0.50789,0.5027,150,150,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
15027,ERR12352456,ERX11729318,ERS17282123,ERP155844,PRJEB70944,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E-MTAB-13603,Transcriptome Analysis,Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals  these changes trigger an adaptive cardiomyocyte hypertrophic response which  if the damage is extensive  will ultimately lead to pathological hypertrophy and heart failure. Conversely  in response to extensive myocardial damage  cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish  changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based  on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals  RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore  using a cyclic cell stretch assay  we have determined that Trpc6a  induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,,Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,Trpc6a KO 7dpa 3,SAMEA114857164,Institut de Génomique Fonctionnelle,ENA FIRST PUBLIC:2023 12 20T00:27:16Z|ENA LAST UPDATE:2023 12 20T00:27:16Z|External Id:SAMEA114857164|INSDC center name:Institut de Génomique Fonctionnelle|INSDC first public:2023 12 20T00:27:16Z|INSDC last update:2023 12 20T00:27:16Z|INSDC status:public|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 3|age:6|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Trpc6a knockout|geographic location country and/or sea:not collected|individual:5 pooled hearts|injury:cardiac resection|isolate:not applicable|organism part:heart|sample name:E MTAB 13603:Trpc6a KO 7dpa 3|scientific name:Danio rerio|sex:mix of males and females|strain:AB,,,,,,,,,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,E MTAB 13603:Trpc6a KO 7dpa 3 p,Trpc6a KO 7dpa 3 p,The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB  Ipswich  MA  USA. Briefly  mRNAs were first enriched with OligodT beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends  and universal adapters were ligated to cDNA fragments  followed by index addition and library enrichment by limited cycle PCR,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP155844,Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch,ENA FIRST PUBLIC:2023 12 20|ENA LAST UPDATE:2023 12 20,6-Trpc6-KO-7dpa_R2_001.fastq.gz 6-Trpc6-KO-7dpa_R1_001.fastq.gz,fastq fastq,10056041651.0,35562752.0,E MTAB 13603:6 Trpc6 KO 7dpa R,0:141.00 1:141.77,A:2670755890;C:2335065805;G:2381199297;T:2659552078;N:9468581,141,141,,,2670755890,2335065805,2381199297,2659552078,9468581,ERX11729318,ERS17282123,ERA27710226,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95324,0.9515,0.07632,0.07479,0.75597,0.75787,0.51981,0.52087,113,113,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2023-12-20,Adult,Adult,Heart,Cardiovascular System
25228,SRR25685572,SRX21410761,SRS18649243,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 14dpi heart3,GSM7717530,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing,zebrafish 14dpi heart3,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717530,GSM7717530: zebrafish 14dpi heart3; Danio rerio; RNA Seq,GSM7717530 r1,GSM7717530,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf4_R1.fq DB14zf4_R2.fq,fastq fastq,571157496.0,7312520.0,GSM7717530 r1,,A:132329616;C:53169305;G:72431948;T:313058610;N:168017,,,,,132329616,53169305,72431948,313058610,168017,SRX21410761,SRS18649243,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.01414,0.679,0.01413,0.08289,1.0,0.98395,,0.48915,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25229,SRR25685573,SRX21410760,SRS18649241,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 14dpi heart2,GSM7717529,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing,zebrafish 14dpi heart2,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717529,GSM7717529: zebrafish 14dpi heart2; Danio rerio; RNA Seq,GSM7717529 r1,GSM7717529,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf3_R1.fq DB14zf3_R2.fq,fastq fastq,97890367.0,1292037.0,GSM7717529 r1,,A:21637243;C:8563955;G:12004508;T:55662880;N:21781,,,,,21637243,8563955,12004508,55662880,21781,SRX21410760,SRS18649241,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.0,0.689,0.0,0.07655,1.0,0.99831,,0.63709,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25230,SRR25685574,SRX21410759,SRS18649242,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 14dpi heart1,GSM7717528,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing,zebrafish 14dpi heart1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717528,GSM7717528: zebrafish 14dpi heart1; Danio rerio; RNA Seq,GSM7717528 r1,GSM7717528,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf1_R1.fq DB14zf1_R2.fq,fastq fastq,1031757474.0,7257847.0,GSM7717528 r1,,A:276216587;C:146620316;G:184052670;T:423474577;N:1393324,,,,,276216587,146620316,184052670,423474577,1393324,SRX21410759,SRS18649242,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.04176,0.6198,0.03023,0.08234,0.99894,0.88885,0.64556,0.53126,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25231,SRR25685575,SRX21410758,SRS18649240,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 7dpi heart3,GSM7717527,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing,zebrafish 7dpi heart3,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi,GSM7717527,GSM7717527: zebrafish 7dpi heart3; Danio rerio; RNA Seq,GSM7717527 r1,GSM7717527,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D37DPIZF3_R1.fq D37DPIZF3_R2.fq,fastq fastq,898901460.0,7585924.0,GSM7717527 r1,,A:236935836;C:100995680;G:128458892;T:431620821;N:890231,,,,,236935836,100995680,128458892,431620821,890231,SRX21410758,SRS18649240,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.12082,0.70068,0.10594,0.1234,0.99983,0.90136,0.875,0.48346,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25232,SRR25685576,SRX21410757,SRS18649239,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 7dpi heart2,GSM7717526,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing,zebrafish 7dpi heart2,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi,GSM7717526,GSM7717526: zebrafish 7dpi heart2; Danio rerio; RNA Seq,GSM7717526 r1,GSM7717526,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D27DPIZF2_R1.fq D27DPIZF2_R2.fq,fastq fastq,1060429257.0,7609110.0,GSM7717526 r1,,A:283107752;C:130181128;G:159305328;T:486464477;N:1370572,,,,,283107752,130181128,159305328,486464477,1370572,SRX21410757,SRS18649239,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.19472,0.68783,0.17584,0.16739,0.99967,0.85628,0.44,0.56319,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25233,SRR25685577,SRX21410756,SRS18649238,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 7dpi heart1,GSM7717525,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing,zebrafish 7dpi heart1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi,GSM7717525,GSM7717525: zebrafish 7dpi heart1; Danio rerio; RNA Seq,GSM7717525 r1,GSM7717525,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D17DPIZF1_R1.fq D17DPIZF1_R2.fq,fastq fastq,1073044507.0,7624815.0,GSM7717525 r1,,A:288576038;C:136858647;G:170330711;T:475869519;N:1409592,,,,,288576038,136858647,170330711,475869519,1409592,SRX21410756,SRS18649238,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.15938,0.70435,0.14583,0.08079,0.99981,0.87949,0.38461,0.57027,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25234,SRR25685578,SRX21410755,SRS18649237,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 3dpi heart3,GSM7717524,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing,zebrafish 3dpi heart3,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi,GSM7717524,GSM7717524: zebrafish 3dpi heart3; Danio rerio; RNA Seq,GSM7717524 r1,GSM7717524,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,FKHEART3_R1.fastq FKHEART3_R2.fastq,fastq fastq,781079621.0,5184230.0,GSM7717524 r1,0:75.26 1:75.40,A:277491111;C:118539142;G:116911958;T:268048500;N:88910,75,75,,,277491111,118539142,116911958,268048500,88910,SRX21410755,SRS18649237,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.04348,0.71869,0.04347,0.28823,1.0,0.79681,,0.53909,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25235,SRR25685579,SRX21410754,SRS18649236,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 3dpi heart2,GSM7717523,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing,zebrafish 3dpi heart2,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi,GSM7717523,GSM7717523: zebrafish 3dpi heart2; Danio rerio; RNA Seq,GSM7717523 r1,GSM7717523,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,FKHEART2_R1.fastq FKHEART2_R2.fastq,fastq fastq,684820059.0,4547520.0,GSM7717523 r1,0:75.21 1:75.38,A:258487418;C:93776953;G:97187917;T:235293267;N:74504,75,75,,,258487418,93776953,97187917,235293267,74504,SRX21410754,SRS18649236,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.09406,0.79542,0.09405,0.0802,1.0,0.83029,,0.56367,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25236,SRR25685580,SRX21410753,SRS18649235,SRP455780,PRJNA1006660,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish],GSE241156,Other,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,zebrafish 3dpi heart1,GSM7717522,,source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing,zebrafish 3dpi heart1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish,adult heart,Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi,GSM7717522,GSM7717522: zebrafish 3dpi heart1; Danio rerio; RNA Seq,GSM7717522 r1,GSM7717522,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,FKHEART1_R1.fastq FKHEART1_R2.fastq,fastq fastq,784558404.0,5209213.0,GSM7717522 r1,0:75.22 1:75.39,A:291009319;C:102718146;G:111606154;T:279144074;N:80711,75,75,,,291009319,102718146,111606154,279144074,80711,SRX21410753,SRS18649235,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.13119,0.82035,0.12871,0.08445,0.99997,0.82785,0.0,0.56254,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25239,SRR25723792,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz,fastq fastq,529790530.0,6160355.0,GSM7728123 r1,0:26 1:60,A:134254092;C:100685793;G:108463112;T:186279563;N:107970,26,60,,,134254092,100685793,108463112,186279563,107970,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11277,0.80912,0.10457,0.43275,0.99131,0.93933,0.67026,0.54274,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25240,SRR25723793,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L002_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L002_R2_001.fastq.gz,fastq fastq,611015122.0,7104827.0,GSM7728123 r2,0:26 1:60,A:152137832;C:116026517;G:127735448;T:214967198;N:148127,26,60,,,152137832,116026517,127735448,214967198,148127,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11413,0.81785,0.10565,0.44205,0.99119,0.93419,0.59743,0.53882,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25241,SRR25723794,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz,fastq fastq,554981822.0,6453277.0,GSM7728123 r3,0:26 1:60,A:140664360;C:105281601;G:113575873;T:195359632;N:100356,26,60,,,140664360,105281601,113575873,195359632,100356,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11352,0.80651,0.10538,0.42971,0.99137,0.93994,0.65893,0.53098,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25242,SRR25723795,SRX21447930,SRS18684553,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 4,GSM7728123,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 4,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728123,GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq,GSM7728123 r1,GSM7728123,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz,fastq fastq,459861436.0,5347226.0,GSM7728123 r4,0:26 1:60,A:115949245;C:86913961;G:95720860;T:161187969;N:89401,26,60,,,115949245,86913961,95720860,161187969,89401,SRX21447930,SRS18684553,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11249,0.81109,0.10407,0.43334,0.99135,0.94034,0.64852,0.53864,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
25243,SRR25723796,SRX21447929,SRS18684552,SRP456323,PRJNA1008049,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq],GSE241390,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,hmga1a mutant plate 3,GSM7728122,,source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing,hmga1a mutant plate 3,Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts,adult heart,cryoinjury was performed 7 days before hearts were extracted,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury,GSM7728122,GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq,GSM7728122 r1,GSM7728122,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,HUB-DB-007_HNWVVBGX9_S6_L001_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L001_R2_001.fastq.gz,fastq fastq,584059454.0,6791389.0,GSM7728122 r1,0:26 1:60,A:162038298;C:107975394;G:118251259;T:195669218;N:125285,26,60,,,162038298,107975394,118251259,195669218,125285,SRX21447929,SRS18684552,SRA1698978,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.08872,0.68673,0.08328,0.37858,0.99346,0.94945,0.60282,0.42608,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System