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55 rows where experiment.platform = "BGISEQ" and tissue_curation = "Heart"

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devstage_curation 4

experiment.library_selection 3

devstage_curation_coarse 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Heart · 55 ✖

technology 1

experiment.platform 1

  • BGISEQ · 55 ✖

experiment.library_strategy 1

experiment.library_source 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
33609 33609 SRR30247666 SRX25709110 SRS22350227 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep3 KO3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep3 hey25nt / replicate 3 hey25nt / replicate 3 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     KO_3_1.fq.gz KO_3_2.fq.gz fastq fastq 6793426200.0 22644754.0 KO 3 1.fq.gz 0:150 1:150 A:1845779030;C:1550159613;G:1539592354;T:1857860950;N:34253 150 150     1845779030 1550159613 1539592354 1857860950 34253 SRX25709110 SRS22350227 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94555 0.92523 0.0631 0.06139 0.76672 0.76968 0.56501 0.57019 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33610 33610 SRR30247667 SRX25709109 SRS22350226 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey25nt / mutantzebrafish hearts at 3 mpf rep2 KO2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep2 hey25nt / replicate 2 hey25nt / replicate 2 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     KO_2_1.fq.gz KO_2_2.fq.gz fastq fastq 6577703400.0 21925678.0 KO 2 1.fq.gz 0:150 1:150 A:1795319867;C:1492750718;G:1485718638;T:1803881133;N:33044 150 150     1795319867 1492750718 1485718638 1803881133 33044 SRX25709109 SRS22350226 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94565 0.92404 0.06212 0.06008 0.77281 0.77546 0.55478 0.56589 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33611 33611 SRR30247668 SRX25709108 SRS22350225 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep1 KO1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep1 hey25nt / replicate 1 hey25nt / replicate 1 RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     KO_1_2.fq.gz KO_1_1.fq.gz fastq fastq 6592159500.0 21973865.0 KO 1 1.fq.gz 0:150 1:150 A:1800707634;C:1491918482;G:1484850929;T:1814648405;N:34050 150 150     1800707634 1491918482 1484850929 1814648405 34050 SRX25709108 SRS22350225 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94443 0.92689 0.06601 0.06488 0.76883 0.77033 0.58332 0.52175 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33612 33612 SRR30247669 SRX25709107 SRS22350224 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep3 WT3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep3 hey2+/+ replicate 3 hey2+/+ replicate 3 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 6582842700.0 21942809.0 WT 3 1.fq.gz 0:150 1:150 A:1796301568;C:1494922823;G:1487154319;T:1804427831;N:36159 150 150     1796301568 1494922823 1487154319 1804427831 36159 SRX25709107 SRS22350224 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94446 0.92023 0.06492 0.06289 0.76694 0.7699 0.55651 0.53407 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33613 33613 SRR30247670 SRX25709106 SRS22350223 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep2 WT2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep2 hey2+/+ replicate 2 hey2+/+ replicate 2 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     WT_2_2.fq.gz WT_2_1.fq.gz fastq fastq 6632526000.0 22108420.0 WT 2 1.fq.gz 0:150 1:150 A:1811392253;C:1505075703;G:1495091968;T:1820928778;N:37298 150 150     1811392253 1505075703 1495091968 1820928778 37298 SRX25709106 SRS22350223 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.94532 0.92096 0.06496 0.06227 0.76564 0.76909 0.56754 0.57117 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
33614 33614 SRR30247671 SRX25709105 SRS22350222 SRP526520 PRJNA1148340 RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts PRJNA1148340 Other To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.       RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep1 WT1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep1 hey2+/+ replicate 1 hey2+/+ replicate 1 RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP526520     WT_1_1.fq.gz WT_1_2.fq.gz fastq fastq 6601461900.0 22004873.0 WT 1 1.fq.gz 0:150 1:150 A:1816453592;C:1485325900;G:1476423985;T:1823223402;N:35021 150 150     1816453592 1485325900 1476423985 1823223402 35021 SRX25709105 SRS22350222 SRA1948261 East China Normal University|School of Life Sciences East China Normal University 2 0.9482 0.92609 0.05744 0.0553 0.77423 0.77699 0.53884 0.54075 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2024-08-15 Adult Adult Heart Cardiovascular System
48009 48009 SRR6910782 SRX3858788 SRS3106147 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart yap sham 3 GSM3070341   tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 3|injury type:Sham Injured|genotype:yap / zebrafish heart yap sham 3 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury sham yap mutant zebrafish heart replicate 3 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Sham Injured|genotype:yap / GSM3070341 GSM3070341: zebrafish heart yap sham 3; Danio rerio; RNA Seq GSM3070341   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070341 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAFRACPEI-39_1.fq.gz fastq 951999850.0 19039997.0 GSM3070341 r1 0:50 A:264195948;C:210535284;G:216206679;T:260149711;N:912228 50       264195948 210535284 216206679 260149711 912228 SRX3858788 SRS3106147 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.94079   0.07209   0.77506   0.57202   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48010 48010 SRR6910781 SRX3858787 SRS3106141 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart yap sham 2 GSM3070340   tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 2|injury type:Sham Injured|genotype:yap / zebrafish heart yap sham 2 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury sham yap mutant zebrafish heart replicate 2 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Sham Injured|genotype:yap / GSM3070340 GSM3070340: zebrafish heart yap sham 2; Danio rerio; RNA Seq GSM3070340   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070340 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAERABPEI-38_1.fq.gz fastq 1422243650.0 28444873.0 GSM3070340 r1 0:50 A:396912878;C:311739320;G:316711298;T:395335784;N:1544370 50       396912878 311739320 316711298 395335784 1544370 SRX3858787 SRS3106141 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.92453   0.08919   0.75402   0.56482   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48011 48011 SRR6910780 SRX3858786 SRS3106146 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart yap sham 1 GSM3070339   tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 1|injury type:Sham Injured|genotype:yap / zebrafish heart yap sham 1 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury sham yap mutant zebrafish heart replicate 1 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Sham Injured|genotype:yap / GSM3070339 GSM3070339: zebrafish heart yap sham 1; Danio rerio; RNA Seq GSM3070339   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070339 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAADRABPEI-35_1.fq.gz fastq 1414732800.0 28294656.0 GSM3070339 r1 0:50 A:382546700;C:323161121;G:333740729;T:373569891;N:1714359 50       382546700 323161121 333740729 373569891 1714359 SRX3858786 SRS3106146 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93663   0.06374   0.78476   0.50181   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48012 48012 SRR6910779 SRX3858785 SRS3106140 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart yap cryo 3 GSM3070338   tissue:7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 3|injury type:Cryoinjured|genotype:yap / zebrafish heart yap cryo 3 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 3 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Cryoinjured|genotype:yap / GSM3070338 GSM3070338: zebrafish heart yap cryo 3; Danio rerio; RNA Seq GSM3070338   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070338 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAALRABPEI-45_1.fq.gz fastq 1417604550.0 28352091.0 GSM3070338 r1 0:50 A:396320928;C:310857539;G:315507312;T:393521845;N:1396926 50       396320928 310857539 315507312 393521845 1396926 SRX3858785 SRS3106140 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93466   0.08509   0.76339   0.55298   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48013 48013 SRR6910778 SRX3858784 SRS3106139 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart yap cryo 2 GSM3070337   tissue:7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 2|injury type:Cryoinjured|genotype:yap / zebrafish heart yap cryo 2 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 2 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Cryoinjured|genotype:yap / GSM3070337 GSM3070337: zebrafish heart yap cryo 2; Danio rerio; RNA Seq GSM3070337   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070337 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAKRABPEI-44_1.fq.gz fastq 1411684000.0 28233680.0 GSM3070337 r1 0:50 A:380723872;C:320871596;G:326847305;T:381926882;N:1314345 50       380723872 320871596 326847305 381926882 1314345 SRX3858784 SRS3106139 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93583   0.07153   0.76209   0.53446   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48014 48014 SRR6910777 SRX3858783 SRS3106138 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart yap cryo 1 GSM3070336   tissue:7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 1|injury type:Cryoinjured|genotype:yap / zebrafish heart yap cryo 1 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 1 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Cryoinjured|genotype:yap / GSM3070336 GSM3070336: zebrafish heart yap cryo 1; Danio rerio; RNA Seq GSM3070336   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070336 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170901_I13_CL100030164_L2_HK500ZEBljgRAAARAAPEI-2_1.fq.gz fastq 983464900.0 19669298.0 GSM3070336 r1 0:50 A:281927620;C:213905948;G:225993312;T:260949314;N:688706 50       281927620 213905948 225993312 260949314 688706 SRX3858783 SRS3106138 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93596   0.08164   0.75753   0.5319   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48015 48015 SRR6910776 SRX3858782 SRS3106137 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart wt sham 3 GSM3070335   tissue:7 xxx post injury sham wildtype zebrafish heart replicate 3|injury type:Sham Injured|genotype:yap +/+ zebrafish heart wt sham 3 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury sham wildtype zebrafish heart replicate 3 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Sham Injured|genotype:yap +/+ GSM3070335 GSM3070335: zebrafish heart wt sham 3; Danio rerio; RNA Seq GSM3070335   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070335 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAACRABPEI-34_1.fq.gz fastq 1422074600.0 28441492.0 GSM3070335 r1 0:50 A:391714900;C:316763778;G:323715902;T:388371260;N:1508760 50       391714900 316763778 323715902 388371260 1508760 SRX3858782 SRS3106137 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93511   0.06875   0.78374   0.5442   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48016 48016 SRR6910775 SRX3858781 SRS3106142 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart wt sham 2 GSM3070334   tissue:7 xxx post injury sham wildtype zebrafish heart replicate 2|injury type:Sham Injured|genotype:yap +/+ zebrafish heart wt sham 2 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury sham wildtype zebrafish heart replicate 2 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Sham Injured|genotype:yap +/+ GSM3070334 GSM3070334: zebrafish heart wt sham 2; Danio rerio; RNA Seq GSM3070334   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070334 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAABRABPEI-32_1.fq.gz fastq 1422698650.0 28453973.0 GSM3070334 r1 0:50 A:393538224;C:315070062;G:319739652;T:393085965;N:1264747 50       393538224 315070062 319739652 393085965 1264747 SRX3858781 SRS3106142 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93436   0.08499   0.76599   0.51331   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48017 48017 SRR6910774 SRX3858780 SRS3106135 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart wt sham 1 GSM3070333   tissue:7 xxx post injury sham wildtype zebrafish heart replicate 1|injury type:Sham Injured|genotype:yap +/+ zebrafish heart wt sham 1 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury sham wildtype zebrafish heart replicate 1 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Sham Injured|genotype:yap +/+ GSM3070333 GSM3070333: zebrafish heart wt sham 1; Danio rerio; RNA Seq GSM3070333   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070333 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAARAAPEI-30_1.fq.gz fastq 1421323500.0 28426470.0 GSM3070333 r1 0:50 A:398883510;C:309497967;G:316648847;T:394532024;N:1761152 50       398883510 309497967 316648847 394532024 1761152 SRX3858780 SRS3106135 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93565   0.0827   0.77749   0.54321   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48018 48018 SRR6910773 SRX3858779 SRS3106136 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart wt cryo 3 GSM3070332   tissue:7 xxx post injury cryoinjury wildtype zebrafish heart replicate 3|injury type:Cryoinjured|genotype:yap +/+ zebrafish heart wt cryo 3 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury cryoinjury wildtype zebrafish heart replicate 3 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Cryoinjured|genotype:yap +/+ GSM3070332 GSM3070332: zebrafish heart wt cryo 3; Danio rerio; RNA Seq GSM3070332   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070332 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAIRABPEI-42_1.fq.gz fastq 1420446700.0 28408934.0 GSM3070332 r1 0:50 A:390252025;C:317481829;G:322013373;T:389237056;N:1462417 50       390252025 317481829 322013373 389237056 1462417 SRX3858779 SRS3106136 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.92817   0.08055   0.75304   0.54626   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48019 48019 SRR6910772 SRX3858778 SRS3106133 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart wt cryo 2 GSM3070331   tissue:7 xxx post injury cryoinjury wildtype zebrafish heart replicate 2|injury type:Cryoinjured|genotype:yap +/+ zebrafish heart wt cryo 2 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury cryoinjury wildtype zebrafish heart replicate 2 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Cryoinjured|genotype:yap +/+ GSM3070331 GSM3070331: zebrafish heart wt cryo 2; Danio rerio; RNA Seq GSM3070331   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070331 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAHRABPEI-41_1.fq.gz fastq 1422338300.0 28446766.0 GSM3070331 r1 0:50 A:393674065;C:315125662;G:322045666;T:389932855;N:1560052 50       393674065 315125662 322045666 389932855 1560052 SRX3858778 SRS3106133 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.9294   0.08412   0.75749   0.52514   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
48020 48020 SRR6910771 SRX3858777 SRS3106134 SRP136723 PRJNA447594 RNAseq of regenerating yap mutant zebrafish hearts GSE112452 Transcriptome Analysis A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.   pubmed:30295714   zebrafish heart wt cryo 1 GSM3070330   tissue:7 xxx post injury cryoinjury wildtype zebrafish heart replicate 1|injury type:Cryoinjured|genotype:yap +/+ zebrafish heart wt cryo 1 Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. "Dirty" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels. 7 xxx post injury cryoinjury wildtype zebrafish heart replicate 1 Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet. injury type:Cryoinjured|genotype:yap +/+ GSM3070330 GSM3070330: zebrafish heart wt cryo 1; Danio rerio; RNA Seq GSM3070330   1 RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol. GEO Accession:GSM3070330 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP136723     170715_I13_CL100028033_L1_HK500ZEBvisRAAGRABPEI-40_1.fq.gz fastq 1419380450.0 28387609.0 GSM3070330 r1 0:50 A:393618390;C:313492075;G:321642338;T:389289283;N:1338364 50       393618390 313492075 321642338 389289283 1338364 SRX3858777 SRS3106134 SRA675997 GEO Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin 1 0.93599   0.08586   0.75381   0.52578   50   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   United States 2018-03-28 Undetermined Adult Heart Cardiovascular System
55977 55977 SRR10895882 SRX7564597 SRS6001804 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 008   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Heart|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 10 CL100101924 L01 10       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_545_2.fq.gz CL100101924_L01_545_1.fq.gz fastq fastq 9098943800.0 90989438.0 CL100101924 L01 545 1.fq.gz 0:100 1:100 A:2494855042;C:2016596912;G:2050775890;T:2525488540;N:11227416 100 100     2494855042 2016596912 2050775890 2525488540 11227416 SRX7564597 SRS6001804 SRA1026516 BGI|BGI-Research BGI 1 0.93737   0.07867   0.76061   0.53141   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Heart Cardiovascular System
55978 55978 SRR10895883 SRX7564596 SRS6001804 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 008   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Heart|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 4 CL100103178 L01 4       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_570_2.fq.gz CL100103178_L01_570_1.fq.gz fastq fastq 6098551000.0 60985510.0 CL100103178 L01 570 1.fq.gz 0:100 1:100 A:1665824009;C:1362170830;G:1387665851;T:1676412762;N:6477548 100 100     1665824009 1362170830 1387665851 1676412762 6477548 SRX7564596 SRS6001804 SRA1026516 BGI|BGI-Research BGI 1 0.9281   0.07522   0.77715   0.52597   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Heart Cardiovascular System
55979 55979 SRR10895884 SRX7564595 SRS6001804 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 008   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Heart|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 3 CL100103178 L01 3       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_568_2.fq.gz CL100103178_L01_568_1.fq.gz fastq fastq 7674097800.0 76740978.0 CL100103178 L01 568 1.fq.gz 0:100 1:100 A:2066126344;C:1741642506;G:1775116741;T:2081782365;N:9429844 100 100     2066126344 1741642506 1775116741 2081782365 9429844 SRX7564595 SRS6001804 SRA1026516 BGI|BGI-Research BGI 1 0.92233   0.07056   0.76029   0.55672   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Heart Cardiovascular System
55980 55980 SRR10895885 SRX7564594 SRS6001804 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 008   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Heart|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 2 CL100103178 L01 2       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_569_1.fq.gz CL100103178_L01_569_2.fq.gz fastq fastq 10407446000.0 104074460.0 CL100103178 L01 569 1.fq.gz 0:100 1:100 A:2806156548;C:2359148121;G:2410612409;T:2819342794;N:12186128 100 100     2806156548 2359148121 2410612409 2819342794 12186128 SRX7564594 SRS6001804 SRA1026516 BGI|BGI-Research BGI 1 0.9202   0.06921   0.77384   0.56843   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Heart Cardiovascular System
55981 55981 SRR10895886 SRX7564593 SRS6001804 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 008   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Heart|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 CL100103178 L01       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_571_2.fq.gz CL100103178_L01_571_1.fq.gz fastq fastq 8778390800.0 87783908.0 CL100103178 L01 571 1.fq.gz 0:100 1:100 A:2364575734;C:1991773326;G:2031934839;T:2379995507;N:10111394 100 100     2364575734 1991773326 2031934839 2379995507 10111394 SRX7564593 SRS6001804 SRA1026516 BGI|BGI-Research BGI 1 0.92192   0.08454   0.7544   0.53692   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Heart Cardiovascular System
57259 57259 SRR11294128 SRX7899687 SRS6307737 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles uninj p53 pos.rep3 GSM4407932   source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles uninj p53 pos.rep3 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of uninjured TgtpWT zebrafish Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407932 GSM4407932: Ventricles uninj p53 pos.rep3; Danio rerio; RNA Seq GSM4407932   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407932 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAADRAAPEI-512_1.fq.gz fastq 1835058950.0 36701179.0 GSM4407932 r1 0:50 A:502113193;C:411542245;G:409297699;T:512105813;N:0 50       502113193 411542245 409297699 512105813 0 SRX7899687 SRS6307737 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93734   0.0825   0.77094   0.54336   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57260 57260 SRR11294127 SRX7899686 SRS6307736 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles uninj p53 pos.rep2 GSM4407931   source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles uninj p53 pos.rep2 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of uninjured TgtpWT zebrafish Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407931 GSM4407931: Ventricles uninj p53 pos.rep2; Danio rerio; RNA Seq GSM4407931   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407931 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAACRAAPEI-511_1.fq.gz fastq 1834865450.0 36697309.0 GSM4407931 r1 0:50 A:505143598;C:405191113;G:410587735;T:513943004;N:0 50       505143598 405191113 410587735 513943004 0 SRX7899686 SRS6307736 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93631   0.08049   0.76481   0.50179   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57261 57261 SRR11294126 SRX7899685 SRS6307735 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles uninj p53 pos.rep1 GSM4407930   source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles uninj p53 pos.rep1 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of uninjured TgtpWT zebrafish Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407930 GSM4407930: Ventricles uninj p53 pos.rep1; Danio rerio; RNA Seq GSM4407930   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407930 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAABRAAPEI-510_1.fq.gz fastq 1834689950.0 36693799.0 GSM4407930 r1 0:50 A:504160420;C:403583740;G:412496526;T:514449264;N:0 50       504160420 403583740 412496526 514449264 0 SRX7899685 SRS6307735 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93629   0.08291   0.77356   0.49244   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57262 57262 SRR11294125 SRX7899684 SRS6307734 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles uninj p53 neg.rep3 GSM4407929   source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles uninj p53 neg.rep3 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of uninjured Tgtp53M214K zebrafish Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407929 GSM4407929: Ventricles uninj p53 neg.rep3; Danio rerio; RNA Seq GSM4407929   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407929 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAIRAAPEI-521_1.fq.gz fastq 1834395600.0 36687912.0 GSM4407929 r1 0:50 A:499900882;C:409384440;G:414252017;T:510858261;N:0 50       499900882 409384440 414252017 510858261 0 SRX7899684 SRS6307734 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93583   0.07847   0.76974   0.54357   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57263 57263 SRR11294124 SRX7899683 SRS6307733 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles uninj p53 neg.rep2 GSM4407928   source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles uninj p53 neg.rep2 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of uninjured Tgtp53M214K zebrafish Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407928 GSM4407928: Ventricles uninj p53 neg.rep2; Danio rerio; RNA Seq GSM4407928   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407928 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAHRAAPEI-520_1.fq.gz fastq 1834233850.0 36684677.0 GSM4407928 r1 0:50 A:504582681;C:405014837;G:412005765;T:512630567;N:0 50       504582681 405014837 412005765 512630567 0 SRX7899683 SRS6307733 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.9324   0.07997   0.77975   0.54924   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57264 57264 SRR11294123 SRX7899682 SRS6307732 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles uninj p53 neg.rep1 GSM4407927   source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles uninj p53 neg.rep1 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of uninjured Tgtp53M214K zebrafish Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407927 GSM4407927: Ventricles uninj p53 neg.rep1; Danio rerio; RNA Seq GSM4407927   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407927 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAGRAAPEI-519_1.fq.gz fastq 1834275500.0 36685510.0 GSM4407927 r1 0:50 A:505039122;C:403354337;G:413206780;T:512675261;N:0 50       505039122 403354337 413206780 512675261 0 SRX7899682 SRS6307732 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93529   0.07696   0.77268   0.49743   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57265 57265 SRR11294122 SRX7899681 SRS6307731 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles inj p53 pos.rep3 GSM4407926   source name:Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes|genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles inj p53 pos.rep3 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407926 GSM4407926: Ventricles inj p53 pos.rep3; Danio rerio; RNA Seq GSM4407926   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407926 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAFRAAPEI-518_1.fq.gz fastq 1835175950.0 36703519.0 GSM4407926 r1 0:50 A:499063627;C:408145558;G:418471943;T:509494822;N:0 50       499063627 408145558 418471943 509494822 0 SRX7899681 SRS6307731 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.92833   0.09812   0.73312   0.51303   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57266 57266 SRR11294121 SRX7899680 SRS6307730 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles inj p53 pos.rep2 GSM4407925   source name:Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes|genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles inj p53 pos.rep2 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407925 GSM4407925: Ventricles inj p53 pos.rep2; Danio rerio; RNA Seq GSM4407925   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407925 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAERAAPEI-517_1.fq.gz fastq 1835814750.0 36716295.0 GSM4407925 r1 0:50 A:502904715;C:405114927;G:414615503;T:513179605;N:0 50       502904715 405114927 414615503 513179605 0 SRX7899680 SRS6307730 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.92779   0.10001   0.73943   0.49706   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57267 57267 SRR11294120 SRX7899679 SRS6307729 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles inj p53 pos.rep1 GSM4407924   source name:Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes|genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles inj p53 pos.rep1 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407924 GSM4407924: Ventricles inj p53 pos.rep1; Danio rerio; RNA Seq GSM4407924   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407924 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAARAAPEI-509_1.fq.gz fastq 1835668100.0 36713362.0 GSM4407924 r1 0:50 A:499256851;C:409731957;G:416052681;T:510626611;N:0 50       499256851 409731957 416052681 510626611 0 SRX7899679 SRS6307729 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.92969   0.10126   0.73417   0.51885   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57268 57268 SRR11294119 SRX7899678 SRS6307728 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles inj p53 neg.rep3 GSM4407923   source name:Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA; tp53M214K zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes|genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA; tp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles inj p53 neg.rep3 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA; tp53M214K zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA; tp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407923 GSM4407923: Ventricles inj p53 neg.rep3; Danio rerio; RNA Seq GSM4407923   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407923 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAALRAAPEI-524_1.fq.gz fastq 1835232550.0 36704651.0 GSM4407923 r1 0:50 A:499303964;C:408224392;G:413995749;T:513708445;N:0 50       499303964 408224392 413995749 513708445 0 SRX7899678 SRS6307728 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93048   0.09466   0.73949   0.4978   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57269 57269 SRR11294118 SRX7899677 SRS6307727 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles inj p53 neg.rep2 GSM4407922   source name:Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA; tp53M214K zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes|genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA; tp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles inj p53 neg.rep2 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA; tp53M214K zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA; tp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407922 GSM4407922: Ventricles inj p53 neg.rep2; Danio rerio; RNA Seq GSM4407922   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407922 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAKRAAPEI-523_1.fq.gz fastq 1835660400.0 36713208.0 GSM4407922 r1 0:50 A:500792390;C:406784182;G:416023927;T:512059901;N:0 50       500792390 406784182 416023927 512059901 0 SRX7899677 SRS6307727 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.92669   0.09942   0.72817   0.51645   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
57270 57270 SRR11294117 SRX7899676 SRS6307726 SRP252540 PRJNA612190 Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration GSE146859 Transcriptome Analysis Transcriptome sequencing of uninjured and regenerating 7dpi tp53M214K and tp53WT ventricles. Overall design: 4 experimental groups were analyzed in triplicates: 1 uninjured ventricle of tp53 mutant fish; 2 injured ventricle of tp53 mutant fish; 3 uninjured ventricle of tp53 wild type fish; 4 injured ventricle of tp53 wild type fish.   pubmed:32877671   Ventricles inj p53 neg.rep1 GSM4407921   source name:Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA; tp53M214K zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes|genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA; tp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles Ventricles inj p53 neg.rep1 RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest Ventricles of TgCmlc2:CreER; β actin2:loxp mCherry STOP loxp DTA; tp53M214K zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes Fish were treated 17 hours with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated. Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. Fish were grown at 28 degrees. Male and female animals between 6 month and 12 month and of 2 cm in length were used. genotype:TgCmlc2:CreER; beta actin2:loxp mCherry STOP loxp DTA; tp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 μM tamoxifen|tissue:Ventricles GSM4407921 GSM4407921: Ventricles inj p53 neg.rep1; Danio rerio; RNA Seq GSM4407921   1 Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra ventricular blood. Atrium and outflow tract were removed and ventricles 5 per sample were homogenized in Trizol using a Tissue Lyser II QIAGEN. RNA was extracted using the standard Trizol protocol genomic DNA removed using RNA clean and Concentrator Kit Zymo Research and processed for libraries preparation. Libraries were constructed by single end 50 bp sequencing with 30 M reads/sample was performed at BGI. RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. DESeq2 v 1.26.0 was employed for differential expression analysis. GEO Accession:GSM4407921 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP252540     CL100137114_L1_HK500ZEBortRAAJRAAPEI-522_1.fq.gz fastq 1835899700.0 36717994.0 GSM4407921 r1 0:50 A:498483398;C:409943675;G:418983494;T:508489133;N:0 50       498483398 409943675 418983494 508489133 0 SRX7899676 SRS6307726 SRA1054226 GEO Poss, Cell Biology, Duke University 1 0.93061   0.09272   0.73762   0.51108   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-12 Adult Adult Heart Cardiovascular System
70178 70178 SRR19568478 SRX15620532 SRS13321067 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         TCDD 4   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:8|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of TCDD treatment TCDD 4 TCDD 4 RNA seq of zebrafish Danio rerio: replicate 4 of TCDD treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     TCDD_4_1.fq.gz TCDD_4_2.fq.gz fastq fastq 6664935600.0 44432904.0 TCDD 4 1.fq.gz 0:150 1:150 A:1778771695;C:1547959320;G:1547444025;T:1790760560;N:0 150 150     1778771695 1547959320 1547444025 1790760560 0 SRX15620532 SRS13321067 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.93639   0.07898   0.67649   0.51984   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70179 70179 SRR19568479 SRX15620531 SRS13321066 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         TCDD 3   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:7|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of TCDD treatment TCDD 3 TCDD 3 RNA seq of zebrafish Danio rerio: replicate 3 of TCDD treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     TCDD_3_1.fq.gz TCDD_3_2.fq.gz fastq fastq 6763596300.0 45090642.0 TCDD 3 1.fq.gz 0:150 1:150 A:1802620229;C:1572061293;G:1575663838;T:1813250940;N:0 150 150     1802620229 1572061293 1575663838 1813250940 0 SRX15620531 SRS13321066 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.93871   0.07491   0.67754   0.51592   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70180 70180 SRR19568480 SRX15620530 SRS13321065 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         TCDD 2   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:6|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of TCDD treatment TCDD 2 TCDD 2 RNA seq of zebrafish Danio rerio: replicate 2 of TCDD treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     TCDD_2_1.fq.gz TCDD_2_2.fq.gz fastq fastq 6628062600.0 44187084.0 TCDD 2 1.fq.gz 0:150 1:150 A:1772545581;C:1536779192;G:1535280305;T:1783457522;N:0 150 150     1772545581 1536779192 1535280305 1783457522 0 SRX15620530 SRS13321065 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.93556   0.07257   0.68067   0.51787   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70181 70181 SRR19568481 SRX15620529 SRS13321064 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         TCDD 1   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:5|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of TCDD treatment TCDD 1 TCDD 1 RNA seq of zebrafish Danio rerio: replicate 1 of TCDD treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     TCDD_1_1.fq.gz TCDD_1_2.fq.gz fastq fastq 6661439100.0 44409594.0 TCDD 1 1.fq.gz 0:150 1:150 A:1776797062;C:1548148693;G:1547340992;T:1789152353;N:0 150 150     1776797062 1548148693 1547340992 1789152353 0 SRX15620529 SRS13321064 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.93716   0.07287   0.67487   0.50549   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70182 70182 SRR19568482 SRX15620528 SRS13321062 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         Ctrl 4   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:4|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of control Ctrl 4 Ctrl 4 RNA seq of zebrafish Danio rerio: replicate 4 of control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     Ctrl_4_1.fq.gz Ctrl_4_2.fq.gz fastq fastq 6737187300.0 44914582.0 Ctrl 4 1.fq.gz 0:150 1:150 A:1792212366;C:1570555803;G:1570692729;T:1803726402;N:0 150 150     1792212366 1570555803 1570692729 1803726402 0 SRX15620528 SRS13321062 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.94104   0.07451   0.67821   0.51308   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70183 70183 SRR19568483 SRX15620527 SRS13321063 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         Ctrl 3   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of control Ctrl 3 Ctrl 3 RNA seq of zebrafish Danio rerio: replicate 3 of control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     Ctrl_3_1.fq.gz Ctrl_3_2.fq.gz fastq fastq 6731291400.0 44875276.0 Ctrl 3 1.fq.gz 0:150 1:150 A:1790044747;C:1568544653;G:1569058962;T:1803643038;N:0 150 150     1790044747 1568544653 1569058962 1803643038 0 SRX15620527 SRS13321063 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.94057   0.06779   0.68162   0.51945   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70184 70184 SRR19568484 SRX15620526 SRS13321060 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         Ctrl 2   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of control Ctrl 2 Ctrl 2 RNA seq of zebrafish Danio rerio: replicate 2 of control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     Ctrl_2_1.fq.gz Ctrl_2_2.fq.gz fastq fastq 6698026800.0 44653512.0 Ctrl 2 1.fq.gz 0:150 1:150 A:1795059523;C:1549817920;G:1547008645;T:1806140712;N:0 150 150     1795059523 1549817920 1547008645 1806140712 0 SRX15620526 SRS13321060 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.93483   0.07839   0.67491   0.52108   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
70185 70185 SRR19568485 SRX15620525 SRS13321061 SRP378839 PRJNA846550 The mechanism of AHR mediated disturbance of lipid metabolism in dioxin induced cardiac development injury in zebrafish PRJNA846550 Other Dioxin like environmental pollutants are chemical substances with persistent ability to cause environmental damage which have a vital impact on the growth and development of human and other organisms. Previous studies have confirmed that dioxin like environmental pollutants are cardiotoxic but the molecular mechanism is still unclear.         Ctrl 1   strain:AB|age:5 dpf|dev stage:5 dpf|sex:not determined|tissue:heart|id:1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio: larval heart of control Ctrl 1 Ctrl 1 RNA seq of zebrafish Danio rerio: replicate 1 of control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP378839     Ctrl_1_1.fq.gz Ctrl_1_2.fq.gz fastq fastq 6735053100.0 44900354.0 Ctrl 1 1.fq.gz 0:150 1:150 A:1769863183;C:1592773959;G:1591379310;T:1781036648;N:0 150 150     1769863183 1592773959 1591379310 1781036648 0 SRX15620525 SRS13321061 SRA1432977 Shandong University|School of basic medical sciences Shandong University 1 0.94397   0.05544   0.69749   0.51432   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-06-07 Larval Larval Heart Cardiovascular System
76452 76452 SRR24950188 SRX20708357 SRS18001302 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments rep1 OE1w1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE1w replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments rep1 OE1w replicate 1 OE1w replicate 1 RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     OE1w1_1.fq.gz OE1w1_2.fq.gz fastq fastq 6792141900.0 22640473.0 OE1w1 1.fq.gz 0:150 1:150 A:1821318465;C:1573309073;G:1556399365;T:1841095017;N:19980 150 150     1821318465 1573309073 1556399365 1841095017 19980 SRX20708357 SRS18001302 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.92576 0.91367 0.07095 0.07022 0.74884 0.75012 0.52564 0.52623 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Juvenile Juvenile Heart Cardiovascular System
76453 76453 SRR24950189 SRX20708356 SRS18001301 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for control littermate hearts at 1 week post 4 HT treatments rep3 CTL1w3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL1w replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for control littermate hearts at 1 week post 4 HT treatments rep3 CTL1w replicate 3 CTL1w replicate 3 RNA Seq for control littermate hearts at 1 week post 4 HT treatments replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     CTL1w3_2.fq.gz CTL1w3_1.fq.gz fastq fastq 6615956700.0 22053189.0 CTL1w3 1.fq.gz 0:150 1:150 A:1790825663;C:1516487260;G:1497904437;T:1810720169;N:19171 150 150     1790825663 1516487260 1497904437 1810720169 19171 SRX20708356 SRS18001301 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.93183 0.91562 0.07118 0.07012 0.7655 0.7682 0.53912 0.52899 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Juvenile Juvenile Heart Cardiovascular System
76454 76454 SRR24950190 SRX20708355 SRS18001300 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for control littermate hearts at 1 week post 4 HT treatments rep2 CTL1w2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL1w replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for control littermate hearts at 1 week post 4 HT treatments rep2 CTL1w replicate 2 CTL1w replicate 2 RNA Seq for control littermate hearts at 1 week post 4 HT treatments replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     CTL1w2_1.fq.gz CTL1w2_2.fq.gz fastq fastq 6582133800.0 21940446.0 CTL1w2 1.fq.gz 0:150 1:150 A:1766322301;C:1524014072;G:1506429130;T:1785350030;N:18267 150 150     1766322301 1524014072 1506429130 1785350030 18267 SRX20708355 SRS18001300 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.93867 0.92389 0.06545 0.06458 0.76357 0.76583 0.53821 0.54255 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Juvenile Juvenile Heart Cardiovascular System
76455 76455 SRR24950191 SRX20708354 SRS18001299 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for control littermate hearts at 1 week post 4 HT treatments rep1 CTL1w1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL1w replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for control littermate hearts at 1 week post 4 HT treatments rep1 CTL1w replicate 1 CTL1w replicate 1 RNA Seq for control littermate hearts at 1 week post 4 HT treatments replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     CTL1w1_2.fq.gz CTL1w1_1.fq.gz fastq fastq 6781172100.0 22603907.0 CTL1w1 1.fq.gz 0:150 1:150 A:1804085074;C:1581571692;G:1567430366;T:1828066356;N:18612 150 150     1804085074 1581571692 1567430366 1828066356 18612 SRX20708354 SRS18001299 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.93867 0.91921 0.06237 0.06146 0.75858 0.76246 0.53972 0.53069 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Juvenile Juvenile Heart Cardiovascular System
76456 76456 SRR24950192 SRX20708353 SRS18001298 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for myocardium specific hey2 overexpressing hearts at 2 month post 4 HT treatments rep3 OE3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for myocardium specific hey2 overexpressing hearts at 1 month post 4 HT treatments rep3 OE replicate 3 OE replicate 3 RNA Seq for myocardium specific hey2 overexpressing hearts at 1 month post 4 HT treatments replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     OE3_1.fq.gz OE3_2.fq.gz fastq fastq 6698218800.0 22327396.0 OE3 1.fq.gz 0:150 1:150 A:1810250125;C:1538223397;G:1526099522;T:1823631856;N:13900 150 150     1810250125 1538223397 1526099522 1823631856 13900 SRX20708353 SRS18001298 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.94309 0.93987 0.07727 0.07734 0.75645 0.75659 0.5045 0.52615 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Adult Adult Heart Cardiovascular System
76457 76457 SRR24950193 SRX20708352 SRS18001297 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for myocardium specific hey2 overexpressing hearts at 2 month post 4 HT treatments rep2 OE2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for myocardium specific hey2 overexpressing hearts at 1 month post 4 HT treatments rep2 OE replicate 2 OE replicate 2 RNA Seq for myocardium specific hey2 overexpressing hearts at 1 month post 4 HT treatments replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     OE2_2.fq.gz OE2_1.fq.gz fastq fastq 6714114300.0 22380381.0 OE2 1.fq.gz 0:150 1:150 A:1821324029;C:1535274751;G:1521032470;T:1836469467;N:13583 150 150     1821324029 1535274751 1521032470 1836469467 13583 SRX20708352 SRS18001297 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.9438 0.94081 0.07627 0.07672 0.75116 0.75221 0.50222 0.53794 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Adult Adult Heart Cardiovascular System
76458 76458 SRR24950194 SRX20708351 SRS18001296 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for myocardium specific hey2 overexpressing hearts at 2 month post 4 HT treatments rep1 OE1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for myocardium specific hey2 overexpressing hearts at 1 month post 4 HT treatments rep1 OE replicate 1 OE replicate 1 RNA Seq for myocardium specific hey2 overexpressing hearts at 1 month post 4 HT treatments replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     OE1_2.fq.gz OE1_1.fq.gz fastq fastq 6717241200.0 22390804.0 OE1 1.fq.gz 0:150 1:150 A:1820907924;C:1536957701;G:1517754438;T:1841608834;N:12303 150 150     1820907924 1536957701 1517754438 1841608834 12303 SRX20708351 SRS18001296 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.94313 0.94062 0.07826 0.07784 0.75526 0.7556 0.52759 0.53976 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Adult Adult Heart Cardiovascular System
76459 76459 SRR24950195 SRX20708350 SRS18001294 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for control littermate hearts at 2 month post 4 HT treatments rep3 CTL3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for control littermate hearts at 1 month post 4 HT treatments rep3 CTL replicate 3 CTL replicate 3 RNA Seq for control littermate hearts at 1 month post 4 HT treatments replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     CTL3_1.fq.gz CTL3_2.fq.gz fastq fastq 6726357300.0 22421191.0 CTL3 1.fq.gz 0:150 1:150 A:1851349315;C:1512108580;G:1497745189;T:1865140192;N:14024 150 150     1851349315 1512108580 1497745189 1865140192 14024 SRX20708350 SRS18001294 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.94596 0.94425 0.06888 0.0684 0.76368 0.76493 0.51461 0.51708 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Adult Adult Heart Cardiovascular System
76460 76460 SRR24950198 SRX20708347 SRS18001292 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments rep3 OE1w3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE1w replicate 3|BioSampleModel:Model organism or animal                 RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments rep3 OE1w replicate 3 OE1w replicate 3 RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     OE1w3_2.fq.gz OE1w3_1.fq.gz fastq fastq 6593130600.0 21977102.0 OE1w3 1.fq.gz 0:150 1:150 A:1770061078;C:1529682678;G:1510949508;T:1782338558;N:98778 150 150     1770061078 1529682678 1510949508 1782338558 98778 SRX20708347 SRS18001292 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.93503 0.922 0.06588 0.06574 0.7503 0.75201 0.52969 0.53743 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Juvenile Juvenile Heart Cardiovascular System
76461 76461 SRR24950199 SRX20708346 SRS18001291 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments rep2 OE1w2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:OE1w replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments rep2 OE1w replicate 2 OE1w replicate 2 RNA Seq for myocardium specific hey2 overexpressing heart at 1 week post 4 HT treatments replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     OE1w2_2.fq.gz OE1w2_1.fq.gz fastq fastq 6742724700.0 22475749.0 OE1w2 1.fq.gz 0:150 1:150 A:1802906309;C:1568304698;G:1553625077;T:1817795677;N:92939 150 150     1802906309 1568304698 1553625077 1817795677 92939 SRX20708346 SRS18001291 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.93354 0.91844 0.06989 0.0686 0.74665 0.74888 0.52723 0.52812 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Juvenile Juvenile Heart Cardiovascular System
76462 76462 SRR24950200 SRX20708345 SRS18001290 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for control littermate hearts at 2 month post 4 HT treatments rep2 CTL2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 2|BioSampleModel:Model organism or animal                 RNA Seq for control littermate hearts at 1 month post 4 HT treatments rep2 CTL replicate 2 CTL replicate 2 RNA Seq for control littermate hearts at 1 month post 4 HT treatments replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     CTL2_2.fq.gz CTL2_1.fq.gz fastq fastq 6733756500.0 22445855.0 CTL2 1.fq.gz 0:150 1:150 A:1852262818;C:1514940822;G:1497196598;T:1869342344;N:13918 150 150     1852262818 1514940822 1497196598 1869342344 13918 SRX20708345 SRS18001290 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.94813 0.94562 0.07048 0.06993 0.76049 0.76039 0.51828 0.52084 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Adult Adult Heart Cardiovascular System
76463 76463 SRR24950201 SRX20708344 SRS18001289 SRP444408 PRJNA984676 RNA Seq analyses of myocardium specific hey2 overexpressing zebrafish hearts and Adv Hey2 infected NRVMs PRJNA984676 Other To elucidate the molecular underpinning of cardiac dilation and myocardial mitochondrial dysfunction caused by hey2 induction we conducted RNA seq analyses in hey2 overexpression zebrafish hearts and control littermate hearts at 1 week or 1 month post 4 HT treatments. To further investigate the impact of Hey2 in mammalian cardiomyocytes and mitochondria we performed comparative analysis of transcriptome profiles on NRVMs infected with adenovirus containing Hey2 Adv Hey2 or vectors Adv Ctrl.       RNA Seq for control littermate hearts at 2 month post 4 HT treatments rep1 CTL1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:male and female|tissue:Heart|ID:CTL replicate 1|BioSampleModel:Model organism or animal                 RNA Seq for control littermate hearts at 1 month post 4 HT treatments rep1 CTL replicate 1 CTL replicate 1 RNA Seq for control littermate hearts at 1 month post 4 HT treatments replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED BGISEQ BGISEQ-500   SRP444408     CTL1_1.fq.gz CTL1_2.fq.gz fastq fastq 6707934300.0 22359781.0 CTL1 1.fq.gz 0:150 1:150 A:1839600655;C:1511741414;G:1501312980;T:1855265253;N:13998 150 150     1839600655 1511741414 1501312980 1855265253 13998 SRX20708344 SRS18001289 SRA1657339 East China Normal University|School of Life Sciences East China Normal University 2 0.94692 0.94575 0.06938 0.06922 0.76613 0.76654 0.51238 0.49316 150 150 B B biological fallback assumption bgi bgi unknown random_priming unknown bulk unknown unknown   China 2023-06-16 Adult Adult Heart Cardiovascular System

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