{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"cDNA\" and experiment.platform = \"BGISEQ\"", "rows": [[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.", null, "pubmed:30295714", null, "zebrafish heart yap sham 3", "GSM3070341", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 264195948, 210535284, 216206679, 260149711, 912228, "SRX3858788", "SRS3106147", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.94079, null, 0.07209, null, 0.77506, null, 0.57202, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart yap sham 2", "GSM3070340", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 396912878, 311739320, 316711298, 395335784, 1544370, "SRX3858787", "SRS3106141", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.92453, null, 0.08919, null, 0.75402, null, 0.56482, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart yap sham 1", "GSM3070339", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 382546700, 323161121, 333740729, 373569891, 1714359, "SRX3858786", "SRS3106146", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93663, null, 0.06374, null, 0.78476, null, 0.50181, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart yap cryo 3", "GSM3070338", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 396320928, 310857539, 315507312, 393521845, 1396926, "SRX3858785", "SRS3106140", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93466, null, 0.08509, null, 0.76339, null, 0.55298, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart yap cryo 2", "GSM3070337", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 380723872, 320871596, 326847305, 381926882, 1314345, "SRX3858784", "SRS3106139", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93583, null, 0.07153, null, 0.76209, null, 0.53446, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart yap cryo 1", "GSM3070336", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 281927620, 213905948, 225993312, 260949314, 688706, "SRX3858783", "SRS3106138", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93596, null, 0.08164, null, 0.75753, null, 0.5319, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart wt sham 3", "GSM3070335", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 391714900, 316763778, 323715902, 388371260, 1508760, "SRX3858782", "SRS3106137", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93511, null, 0.06875, null, 0.78374, null, 0.5442, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart wt sham 2", "GSM3070334", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 393538224, 315070062, 319739652, 393085965, 1264747, "SRX3858781", "SRS3106142", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93436, null, 0.08499, null, 0.76599, null, 0.51331, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart wt sham 1", "GSM3070333", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 398883510, 309497967, 316648847, 394532024, 1761152, "SRX3858780", "SRS3106135", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93565, null, 0.0827, null, 0.77749, null, 0.54321, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart wt cryo 3", "GSM3070332", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 390252025, 317481829, 322013373, 389237056, 1462417, "SRX3858779", "SRS3106136", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.92817, null, 0.08055, null, 0.75304, null, 0.54626, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart wt cryo 2", "GSM3070331", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 393674065, 315125662, 322045666, 389932855, 1560052, "SRX3858778", "SRS3106133", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.9294, null, 0.08412, null, 0.75749, null, 0.52514, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:30295714", null, "zebrafish heart wt cryo 1", "GSM3070330", null, "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", null, "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", null, "SRP136723", null, null, "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, null, null, null, 393618390, 313492075, 321642338, 389289283, 1338364, "SRX3858777", "SRS3106134", "SRA675997", "GEO", "Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin", 1, 0.93599, null, 0.08586, null, 0.75381, null, 0.52578, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-03-28", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [48812, "SRR7341816", "SRX4215318", "SRS3417596", "SRP150521", "PRJNA476105", "Transcriptome analysis of wildtype and sox3 /  zebrafish adult ovary", "GSE115806", "Transcriptome Analysis", "The goals of this study are to compare the differentially expressed genes between wildtype and sox3 /  zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT\u2013PCR. Further  the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 /  zebrafish were generated by deep sequencing.", null, "pubmed:30588557", null, "KO mix", "GSM3190267", null, "source name:Ovary|strain:AB|tissue:Ovary|age:Adult", "KO mix", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz10 whole genome using HISAT  mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.", "Ovary", null, "Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", null, "strain:AB|tissue:Ovary|age:Adult", "GSM3190267", "GSM3190267: KO mix; Danio rerio; RNA Seq", "GSM3190267", null, "1", "Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", "GEO Accession:GSM3190267", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP150521", null, null, "KO-ovary.fq.gz", "fastq", 1173123100.0, 23462462.0, "GSM3190267 r1", "0:50 1:0", "A:308426188;C:271468505;G:292019086;T:300532126;N:677195", 50, 0, null, null, 308426188, 271468505, 292019086, 300532126, 677195, "SRX4215318", "SRS3417596", "SRA721702", "GEO", "Wuhan university", 1, 0.93261, null, 0.02261, null, 0.76132, null, 0.4585, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-06-14", "Adult", "Adult", "Gonad", "Reproductive System"], [48813, "SRR7341815", "SRX4215317", "SRS3417595", "SRP150521", "PRJNA476105", "Transcriptome analysis of wildtype and sox3 /  zebrafish adult ovary", "GSE115806", "Transcriptome Analysis", "The goals of this study are to compare the differentially expressed genes between wildtype and sox3 /  zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT\u2013PCR. Further  the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 /  zebrafish were generated by deep sequencing.", null, "pubmed:30588557", null, "WT mix", "GSM3190266", null, "source name:Ovary|strain:AB|tissue:Ovary|age:Adult", "WT mix", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz10 whole genome using HISAT  mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.", "Ovary", null, "Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", null, "strain:AB|tissue:Ovary|age:Adult", "GSM3190266", "GSM3190266: WT mix; Danio rerio; RNA Seq", "GSM3190266", null, "1", "Ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", "GEO Accession:GSM3190266", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP150521", null, null, "WT-ovary.fq.gz", "fastq", 1176463600.0, 23529272.0, "GSM3190266 r1", "0:50 1:0", "A:311869864;C:270650722;G:289863261;T:303489229;N:590524", 50, 0, null, null, 311869864, 270650722, 289863261, 303489229, 590524, "SRX4215317", "SRS3417595", "SRA721702", "GEO", "Wuhan university", 1, 0.93489, null, 0.02765, null, 0.75627, null, 0.46875, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-06-14", "Adult", "Adult", "Gonad", "Reproductive System"], [50717, "SRR8257205", "SRX5074433", "SRS4088243", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 3", "GSM3494529", null, "tissue:whole embryo|developmental stage:36hpf|genotype:WT", "RNAseq in zebrafish wild type embryos at 36hpf replicate 3", "Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:WT", "GSM3494529", "GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq", "GSM3494529", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_WT_36hpf_rep3.fq.gz", "fastq", 2560587500.0, 51211750.0, "GSM3494529 r1", "0:50", "A:719232941;C:550474431;G:576590260;T:714289868;N:0", 50, null, null, null, 719232941, 550474431, 576590260, 714289868, 0, "SRX5074433", "SRS4088243", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93981, null, 0.10951, null, 0.71388, null, 0.48297, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50718, "SRR8257204", "SRX5074432", "SRS4088242", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 2", "GSM3494528", null, "tissue:whole embryo|developmental stage:36hpf|genotype:WT", "RNAseq in zebrafish wild type embryos at 36hpf replicate 2", "Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:WT", "GSM3494528", "GSM3494528: RNAseq in zebrafish wild type embryos at 36hpf replicate 2; Danio rerio; RNA Seq", "GSM3494528", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_WT_36hpf_rep2.fq.gz", "fastq", 2775840750.0, 55516815.0, "GSM3494528 r1", "0:50", "A:783053027;C:587947172;G:603351259;T:801489292;N:0", 50, null, null, null, 783053027, 587947172, 603351259, 801489292, 0, "SRX5074432", "SRS4088242", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93386, null, 0.11853, null, 0.7007, null, 0.48856, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50719, "SRR8257203", "SRX5074431", "SRS4088241", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 1", "GSM3494527", null, "tissue:whole embryo|developmental stage:36hpf|genotype:WT", "RNAseq in zebrafish wild type embryos at 36hpf replicate 1", "Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:WT", "GSM3494527", "GSM3494527: RNAseq in zebrafish wild type embryos at 36hpf replicate 1; Danio rerio; RNA Seq", "GSM3494527", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_WT_36hpf_rep1.fq.gz", "fastq", 2638769750.0, 52775395.0, "GSM3494527 r1", "0:50", "A:749627286;C:556213831;G:574654547;T:758274086;N:0", 50, null, null, null, 749627286, 556213831, 574654547, 758274086, 0, "SRX5074431", "SRS4088241", "SRA815839", "GEO", "CABD/CSIC", 1, 0.92992, null, 0.12022, null, 0.72174, null, 0.49097, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50720, "SRR8257202", "SRX5074430", "SRS4088240", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3", "GSM3494526", null, "tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ", "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3", "Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:tp63  / ", "GSM3494526", "GSM3494526: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3; Danio rerio; RNA Seq", "GSM3494526", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_p63mut_36hpf_rep3.fq.gz", "fastq", 2651169450.0, 53023389.0, "GSM3494526 r1", "0:50", "A:752539060;C:560162268;G:581624300;T:756843822;N:0", 50, null, null, null, 752539060, 560162268, 581624300, 756843822, 0, "SRX5074430", "SRS4088240", "SRA815839", "GEO", "CABD/CSIC", 1, 0.94022, null, 0.12949, null, 0.70019, null, 0.50336, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50721, "SRR8257201", "SRX5074429", "SRS4088239", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2", "GSM3494525", null, "tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ", "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2", "Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:tp63  / ", "GSM3494525", "GSM3494525: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2; Danio rerio; RNA Seq", "GSM3494525", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_p63mut_36hpf_rep2.fq.gz", "fastq", 2821501700.0, 56430034.0, "GSM3494525 r1", "0:50", "A:795357588;C:599294949;G:620563224;T:806285939;N:0", 50, null, null, null, 795357588, 599294949, 620563224, 806285939, 0, "SRX5074429", "SRS4088239", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93671, null, 0.12314, null, 0.6957, null, 0.48362, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50722, "SRR8257200", "SRX5074428", "SRS4088238", "SRP171045", "PRJNA507426", "Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]", "GSE123058", "Transcriptome Analysis", "The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program  its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here  we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development  we found two distinct functions clearly separated in space and time. During early development  p63 binds enhancers associated to neural genes  where it limits Sox3 binding and reduces the expression of these neural genes. Indeed  we show that p63 and Sox3 are co expressed in the neural plate border. Later in development  p63 binds enhancers associated to epidermal genes and promotes their expression  acting as a pioneer factor  as it binds to non accessible chromatin and is required for its opening. Therefore  our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification  promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants", "parent bioproject:PRJNA507423", "pubmed:31296872", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1", "GSM3494524", null, "tissue:whole embryo|developmental stage:36hpf|genotype:tp63  / ", "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1", "Reads were aligned against reference genome using STAR software  and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:36hpf|genotype:tp63  / ", "GSM3494524", "GSM3494524: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1; Danio rerio; RNA Seq", "GSM3494524", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM3494524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP171045", null, null, "RNAseq_zebra_p63mut_36hpf_rep1.fq.gz", "fastq", 2592494100.0, 51849882.0, "GSM3494524 r1", "0:50", "A:730978948;C:550803197;G:572081489;T:738630466;N:0", 50, null, null, null, 730978948, 550803197, 572081489, 738630466, 0, "SRX5074428", "SRS4088238", "SRA815839", "GEO", "CABD/CSIC", 1, 0.94035, null, 0.11571, null, 0.70796, null, 0.49468, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [52944, "SRR9609439", "SRX6372833", "SRS5033898", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 3", "GSM3909672", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909672", "GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq", "GSM3909672", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909672", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1283013300.0, 25660266.0, "GSM3909672 r1", "0:50", "A:339417002;C:304649204;G:297783450;T:341163644;N:0", 50, null, null, null, 339417002, 304649204, 297783450, 341163644, 0, "SRX6372833", "SRS5033898", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94342, null, 0.10559, null, 0.72401, null, 0.47431, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52945, "SRR9609438", "SRX6372832", "SRS5033897", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 2", "GSM3909671", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909671", "GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq", "GSM3909671", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909671", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1282475700.0, 25649514.0, "GSM3909671 r1", "0:50", "A:339635626;C:302447093;G:295507893;T:344885088;N:0", 50, null, null, null, 339635626, 302447093, 295507893, 344885088, 0, "SRX6372832", "SRS5033897", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94396, null, 0.10502, null, 0.71465, null, 0.47566, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52946, "SRR9609437", "SRX6372831", "SRS5033896", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "PBCAB Replicate 1", "GSM3909670", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB", "PBCAB Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909670", "GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq", "GSM3909670", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909670", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1147572700.0, 22951454.0, "GSM3909670 r1", "0:50", "A:300633532;C:273711082;G:268229512;T:304998574;N:0", 50, null, null, null, 300633532, 273711082, 268229512, 304998574, 0, "SRX6372831", "SRS5033896", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94418, null, 0.09965, null, 0.72746, null, 0.47644, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52947, "SRR9609436", "SRX6372830", "SRS5033895", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 3", "GSM3909669", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909669", "GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq", "GSM3909669", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909669", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1282414400.0, 25648288.0, "GSM3909669 r1", "0:50", "A:334687310;C:307161534;G:302070174;T:338495382;N:0", 50, null, null, null, 334687310, 307161534, 302070174, 338495382, 0, "SRX6372830", "SRS5033895", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94359, null, 0.09476, null, 0.72529, null, 0.47117, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52948, "SRR9609435", "SRX6372829", "SRS5033894", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 2", "GSM3909668", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909668", "GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq", "GSM3909668", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909668", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1281370000.0, 25627400.0, "GSM3909668 r1", "0:50", "A:335735118;C:306450529;G:298815464;T:340368889;N:0", 50, null, null, null, 335735118, 306450529, 298815464, 340368889, 0, "SRX6372829", "SRS5033894", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94338, null, 0.09412, null, 0.7204, null, 0.48662, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52949, "SRR9609434", "SRX6372828", "SRS5033893", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "NF YA DN Replicate 1", "GSM3909667", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN", "NF YA DN Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909667", "GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq", "GSM3909667", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909667", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1278504750.0, 25570095.0, "GSM3909667 r1", "0:50", "A:334370606;C:306252389;G:299065406;T:338816349;N:0", 50, null, null, null, 334370606, 306252389, 299065406, 338816349, 0, "SRX6372828", "SRS5033893", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94373, null, 0.09279, null, 0.7191, null, 0.48836, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52950, "SRR9609433", "SRX6372827", "SRS5033892", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 3", "GSM3909666", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 3", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909666", "GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq", "GSM3909666", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909666", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate3.fq.gz", "fastq", 1284828600.0, 25696572.0, "GSM3909666 r1", "0:50", "A:340467505;C:302914392;G:291984238;T:349462465;N:0", 50, null, null, null, 340467505, 302914392, 291984238, 349462465, 0, "SRX6372827", "SRS5033892", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94288, null, 0.0963, null, 0.71713, null, 0.4793, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52951, "SRR9609432", "SRX6372826", "SRS5033891", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 2", "GSM3909665", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 2", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909665", "GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq", "GSM3909665", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909665", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate2.fq.gz", "fastq", 1274433150.0, 25488663.0, "GSM3909665 r1", "0:50", "A:336050330;C:303141446;G:297353928;T:337887446;N:0", 50, null, null, null, 336050330, 303141446, 297353928, 337887446, 0, "SRX6372826", "SRS5033891", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94266, null, 0.0966, null, 0.72476, null, 0.47615, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [52952, "SRR9609431", "SRX6372825", "SRS5033890", "SRP212216", "PRJNA551488", "TALE  and NF Y dependent Genes in 12 hpf Zebrafish Embryos", "GSE133459", "Transcriptome Analysis", "In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB  we find 646 downregulated and 854 upregulated genes. For NF YA DN  we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription  development  and homeodomain ontologies  while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription  development  and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.", null, null, null, "GFP Replicate 1", "GSM3909664", null, "tissue:Whole Embryo|Stage:12 hpf|treatment:GFP", "GFP Replicate 1", "Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters  p4   bowtie e 70   bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.", "Whole Embryo", "Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA  0.1% phenol red  and water. The mRNAs encoded either a dominant negative Pbx PBCAB  dominant negative NF YA NF YA DN  or GFP control.", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "Injected embryos were raised to 12 hours in egg water 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909664", "GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq", "GSM3909664", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30\u03bcL of water. Sample quality was assessed on a Bioanalyzer Agilent  with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI  Inc. Polyadenylated RNAs were selected using oligo dT beads  fragmented  and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.", "GEO Accession:GSM3909664", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP212216", null, null, "GFP_12hpf_zebrafish_biological_replicate1.fq.gz", "fastq", 1278273350.0, 25565467.0, "GSM3909664 r1", "0:50", "A:336762127;C:304299745;G:297929933;T:339281545;N:0", 50, null, null, null, 336762127, 304299745, 297929933, 339281545, 0, "SRX6372825", "SRS5033890", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94207, null, 0.09472, null, 0.72642, null, 0.47988, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [57168, "SRR11237928", "SRX7849591", "SRS6259054", "SRP251591", "PRJNA610302", "Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development", "GSE146394", "Transcriptome Analysis", "To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology", null, null, null, "MZ 7hpf Dome", "GSM4379949", null, "source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ", "MZ 7hpf Dome", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", null, "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ", "GSM4379949", "GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq", "GSM4379949", null, "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", "GEO Accession:GSM4379949", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP251591", null, null, "MZ_7h_Dome_1.fq.gz", "fastq", 1065702100.0, 21314042.0, "GSM4379949 r1", "0:50 1:0", "A:283324952;C:247492025;G:242059243;T:291819466;N:1006414", 50, 0, null, null, 283324952, 247492025, 242059243, 291819466, 1006414, "SRX7849591", "SRS6259054", "SRA1051151", "GEO", "School of life science, Tsinghua University", 1, 0.9445, null, 0.07752, null, 0.72565, null, 0.4828, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [57169, "SRR11237927", "SRX7849590", "SRS6259053", "SRP251591", "PRJNA610302", "Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development", "GSE146394", "Transcriptome Analysis", "To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology", null, null, null, "MZ 4.3hpf 1k", "GSM4379948", null, "source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ", "MZ 4.3hpf 1k", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", null, "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ", "GSM4379948", "GSM4379948: MZ 4.3hpf 1k; Danio rerio; RNA Seq", "GSM4379948", null, "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", "GEO Accession:GSM4379948", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP251591", null, null, "MZ_4.3h_1k_1.fq.gz", "fastq", 1059959500.0, 21199190.0, "GSM4379948 r1", "0:50 1:0", "A:278456455;C:249622199;G:244991579;T:285847713;N:1041554", 50, 0, null, null, 278456455, 249622199, 244991579, 285847713, 1041554, "SRX7849590", "SRS6259053", "SRA1051151", "GEO", "School of life science, Tsinghua University", 1, 0.94882, null, 0.03659, null, 0.74361, null, 0.48435, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [57170, "SRR11237926", "SRX7849589", "SRS6259052", "SRP251591", "PRJNA610302", "Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development", "GSE146394", "Transcriptome Analysis", "To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology", null, null, null, "WT 4.3hpf Dome", "GSM4379947", null, "source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type", "WT 4.3hpf Dome", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", null, "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type", "GSM4379947", "GSM4379947: WT 4.3hpf Dome; Danio rerio; RNA Seq", "GSM4379947", null, "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", "GEO Accession:GSM4379947", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP251591", null, null, "WT_4.3h_Dome_1.fq.gz", "fastq", 1058158950.0, 21163179.0, "GSM4379947 r1", "0:50 1:0", "A:279307143;C:247873321;G:244308380;T:285580565;N:1089541", 50, 0, null, null, 279307143, 247873321, 244308380, 285580565, 1089541, "SRX7849589", "SRS6259052", "SRA1051151", "GEO", "School of life science, Tsinghua University", 1, 0.94374, null, 0.05294, null, 0.74164, null, 0.48705, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:32877671", null, "Ventricles  uninj p53 pos.rep3", "GSM4407932", null, "source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 \u03bcM 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407932", "GSM4407932: Ventricles  uninj p53 pos.rep3; Danio rerio; RNA Seq", "GSM4407932", null, "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", null, "SRP252540", null, null, "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, null, null, null, 502113193, 411542245, 409297699, 512105813, 0, "SRX7899687", "SRS6307737", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93734, null, 0.0825, null, 0.77094, null, 0.54336, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  uninj p53 pos.rep2", "GSM4407931", null, "source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 \u03bcM 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407931", "GSM4407931: Ventricles  uninj p53 pos.rep2; Danio rerio; RNA Seq", "GSM4407931", null, "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", null, "SRP252540", null, null, "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, null, null, null, 505143598, 405191113, 410587735, 513943004, 0, "SRX7899686", "SRS6307736", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93631, null, 0.08049, null, 0.76481, null, 0.50179, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  uninj p53 pos.rep1", "GSM4407930", null, "source name:Ventricles of uninjured TgtpWT zebrafish|genotype:Tgtp53WT|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 \u03bcM 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407930", "GSM4407930: Ventricles  uninj p53 pos.rep1; Danio rerio; RNA Seq", "GSM4407930", null, "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", null, "SRP252540", null, null, "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, null, null, null, 504160420, 403583740, 412496526, 514449264, 0, "SRX7899685", "SRS6307735", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93629, null, 0.08291, null, 0.77356, null, 0.49244, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  uninj p53 neg.rep3", "GSM4407929", null, "source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 \u03bcM 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407929", "GSM4407929: Ventricles  uninj p53 neg.rep3; Danio rerio; RNA Seq", "GSM4407929", null, "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", null, "SRP252540", null, null, "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, null, null, null, 499900882, 409384440, 414252017, 510858261, 0, "SRX7899684", "SRS6307734", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93583, null, 0.07847, null, 0.76974, null, 0.54357, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  uninj p53 neg.rep2", "GSM4407928", null, "source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 \u03bcM 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407928", "GSM4407928: Ventricles  uninj p53 neg.rep2; Danio rerio; RNA Seq", "GSM4407928", null, "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", null, "SRP252540", null, null, "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, null, null, null, 504582681, 405014837, 412005765, 512630567, 0, "SRX7899683", "SRS6307733", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.9324, null, 0.07997, null, 0.77975, null, 0.54924, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  uninj p53 neg.rep1", "GSM4407927", null, "source name:Ventricles of uninjured Tgtp53M214K zebrafish|genotype:Tgtp53M214K|strain:EK /AB strain|treatment: 17 hours treatment with 0.5 \u03bcM 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407927", "GSM4407927: Ventricles  uninj p53 neg.rep1; Danio rerio; RNA Seq", "GSM4407927", null, "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", null, "SRP252540", null, null, "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, null, null, null, 505039122, 403354337, 413206780, 512675261, 0, "SRX7899682", "SRS6307732", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93529, null, 0.07696, null, 0.77268, null, 0.49743, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  inj p53 pos.rep3", "GSM4407926", null, "source name:Ventricles of TgCmlc2:CreER; \u03b2 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 \u03bcM 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; \u03b2 actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes", "Fish were treated  17 hours  with 0.5 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407926", "GSM4407926: Ventricles  inj p53 pos.rep3; Danio rerio; RNA Seq", "GSM4407926", null, "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", null, "SRP252540", null, null, "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, null, null, null, 499063627, 408145558, 418471943, 509494822, 0, "SRX7899681", "SRS6307731", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92833, null, 0.09812, null, 0.73312, null, 0.51303, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  inj p53 pos.rep2", "GSM4407925", null, "source name:Ventricles of TgCmlc2:CreER; \u03b2 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 \u03bcM 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; \u03b2 actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes", "Fish were treated  17 hours  with 0.5 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407925", "GSM4407925: Ventricles  inj p53 pos.rep2; Danio rerio; RNA Seq", "GSM4407925", null, "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", null, "SRP252540", null, null, "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, null, null, null, 502904715, 405114927, 414615503, 513179605, 0, "SRX7899680", "SRS6307730", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92779, null, 0.10001, null, 0.73943, null, 0.49706, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  inj p53 pos.rep1", "GSM4407924", null, "source name:Ventricles of TgCmlc2:CreER; \u03b2 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 \u03bcM 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; \u03b2 actin2:loxp mCherry STOP loxp DTA zebrafish 7 days post tamoxifen induced genetic ablation of cardiomyocytes", "Fish were treated  17 hours  with 0.5 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407924", "GSM4407924: Ventricles  inj p53 pos.rep1; Danio rerio; RNA Seq", "GSM4407924", null, "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", null, "SRP252540", null, null, "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, null, null, null, 499256851, 409731957, 416052681, 510626611, 0, "SRX7899679", "SRS6307729", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92969, null, 0.10126, null, 0.73417, null, 0.51885, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  inj p53 neg.rep3", "GSM4407923", null, "source name:Ventricles of TgCmlc2:CreER; \u03b2 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 \u03bcM 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; \u03b2 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407923", "GSM4407923: Ventricles  inj p53 neg.rep3; Danio rerio; RNA Seq", "GSM4407923", null, "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", null, "SRP252540", null, null, "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, null, null, null, 499303964, 408224392, 413995749, 513708445, 0, "SRX7899678", "SRS6307728", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93048, null, 0.09466, null, 0.73949, null, 0.4978, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  inj p53 neg.rep2", "GSM4407922", null, "source name:Ventricles of TgCmlc2:CreER; \u03b2 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 \u03bcM 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; \u03b2 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407922", "GSM4407922: Ventricles  inj p53 neg.rep2; Danio rerio; RNA Seq", "GSM4407922", null, "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", null, "SRP252540", null, null, "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, null, null, null, 500792390, 406784182, 416023927, 512059901, 0, "SRX7899677", "SRS6307727", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.92669, null, 0.09942, null, 0.72817, null, 0.51645, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [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.", null, "pubmed:32877671", null, "Ventricles  inj p53 neg.rep1", "GSM4407921", null, "source name:Ventricles of TgCmlc2:CreER; \u03b2 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 \u03bcM 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; \u03b2 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 \u03bcM 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 \u03bcM tamoxifen|tissue:Ventricles", "GSM4407921", "GSM4407921: Ventricles  inj p53 neg.rep1; Danio rerio; RNA Seq", "GSM4407921", null, "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", null, "SRP252540", null, null, "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, null, null, null, 498483398, 409943675, 418983494, 508489133, 0, "SRX7899676", "SRS6307726", "SRA1054226", "GEO", "Poss, Cell Biology, Duke University", 1, 0.93061, null, 0.09272, null, 0.73762, null, 0.51108, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-12", "Adult", "Adult", "Heart", "Cardiovascular System"], [60605, "SRR12435896", "SRX8931591", "SRS7187999", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  replicate 2", "GSM4724538", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 48hpf  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT", "GSM4724538", "GSM4724538: RNA seq in zebrafish wild type embryos at 48hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724538", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724538", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_rep2_1.fq.gz", "fastq", 2857833100.0, 57156662.0, "GSM4724538 r1", "0:50 1:0", "A:833205284;C:613960566;G:684040839;T:726626411;N:0", 50, 0, null, null, 833205284, 613960566, 684040839, 726626411, 0, "SRX8931591", "SRS7187999", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94607, null, 0.13254, null, 0.683, null, 0.47253, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60606, "SRR12435895", "SRX8931590", "SRS7187998", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  replicate 1", "GSM4724537", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 48hpf  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT", "GSM4724537", "GSM4724537: RNA seq in zebrafish wild type embryos at 48hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724537", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724537", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_rep1_1.fq.gz", "fastq", 1780117200.0, 35602344.0, "GSM4724537 r1", "0:50 1:0", "A:515966090;C:381813611;G:432619671;T:449717828;N:0", 50, 0, null, null, 515966090, 381813611, 432619671, 449717828, 0, "SRX8931590", "SRS7187998", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95016, null, 0.1291, null, 0.68546, null, 0.47379, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60607, "SRR12435894", "SRX8931589", "SRS7187997", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2", "GSM4724536", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "GSM4724536", "GSM4724536: RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2; Danio rerio; RNA Seq", "GSM4724536", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724536", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_p53MO_rep2_1.fq.gz", "fastq", 1604734300.0, 32094686.0, "GSM4724536 r1", "0:50", "A:420858899;C:372944640;G:386038616;T:424892145;N:0", 50, null, null, null, 420858899, 372944640, 386038616, 424892145, 0, "SRX8931589", "SRS7187997", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.9522, null, 0.09133, null, 0.68885, null, 0.47214, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60608, "SRR12435893", "SRX8931588", "SRS7187996", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1", "GSM4724535", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino", "GSM4724535", "GSM4724535: RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1; Danio rerio; RNA Seq", "GSM4724535", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724535", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_wt_p53MO_rep1_1.fq.gz", "fastq", 2384014500.0, 47680290.0, "GSM4724535 r1", "0:50", "A:625164876;C:552875690;G:576784849;T:629189085;N:0", 50, null, null, null, 625164876, 552875690, 576784849, 629189085, 0, "SRX8931588", "SRS7187996", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94749, null, 0.09167, null, 0.67978, null, 0.48327, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60609, "SRR12435892", "SRX8931587", "SRS7187995", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2", "GSM4724534", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / ", "GSM4724534", "GSM4724534: RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724534", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724534", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_rep2_1.fq.gz", "fastq", 2142745700.0, 42854914.0, "GSM4724534 r1", "0:50 1:0", "A:622717093;C:460353664;G:518363295;T:541311648;N:0", 50, 0, null, null, 622717093, 460353664, 518363295, 541311648, 0, "SRX8931587", "SRS7187995", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94287, null, 0.14736, null, 0.69199, null, 0.47986, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60610, "SRR12435891", "SRX8931586", "SRS7187994", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1", "GSM4724533", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / ", "GSM4724533", "GSM4724533: RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724533", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724533", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_rep1_1.fq.gz", "fastq", 1858500400.0, 37170008.0, "GSM4724533 r1", "0:50 1:0", "A:544611701;C:398699344;G:449892006;T:465297349;N:0", 50, 0, null, null, 544611701, 398699344, 449892006, 465297349, 0, "SRX8931586", "SRS7187994", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94363, null, 0.14349, null, 0.69089, null, 0.48114, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60611, "SRR12435890", "SRX8931585", "SRS7187993", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2", "GSM4724532", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "GSM4724532", "GSM4724532: RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2; Danio rerio; RNA Seq", "GSM4724532", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724532", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_p53MO_rep2_1.fq.gz", "fastq", 2622498950.0, 52449979.0, "GSM4724532 r1", "0:50", "A:683425987;C:612438973;G:639683260;T:686950730;N:0", 50, null, null, null, 683425987, 612438973, 639683260, 686950730, 0, "SRX8931585", "SRS7187993", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94822, null, 0.10163, null, 0.69954, null, 0.4758, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60612, "SRR12435889", "SRX8931584", "SRS7187992", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1", "GSM4724531", null, "tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:48 hpf|genotype:ctcf  / |treatment:tp53 morpholino", "GSM4724531", "GSM4724531: RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1; Danio rerio; RNA Seq", "GSM4724531", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724531", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_48h_ctcf_p53MO_rep1_1.fq.gz", "fastq", 2421682100.0, 48433642.0, "GSM4724531 r1", "0:50", "A:625808320;C:568572947;G:596940410;T:630360423;N:0", 50, null, null, null, 625808320, 568572947, 596940410, 630360423, 0, "SRX8931584", "SRS7187992", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94893, null, 0.09731, null, 0.71476, null, 0.48546, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [60613, "SRR12435888", "SRX8931583", "SRS7187991", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 24hpf  replicate 2", "GSM4724530", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 24hpf  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:24 hpf|genotype:WT", "GSM4724530", "GSM4724530: RNA seq in zebrafish wild type embryos at 24hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724530", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724530", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_wt_rep2_1.fq.gz", "fastq", 2241073250.0, 44821465.0, "GSM4724530 r1", "0:50", "A:593435654;C:517470954;G:544866646;T:585299996;N:0", 50, null, null, null, 593435654, 517470954, 544866646, 585299996, 0, "SRX8931583", "SRS7187991", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.9534, null, 0.07821, null, 0.70331, null, 0.47463, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [60614, "SRR12435887", "SRX8931582", "SRS7187990", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish wild type embryos at 24hpf  replicate 1", "GSM4724529", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:WT", "RNA seq in zebrafish wild type embryos at 24hpf  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:24 hpf|genotype:WT", "GSM4724529", "GSM4724529: RNA seq in zebrafish wild type embryos at 24hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724529", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_wt_rep1_1.fq.gz", "fastq", 1206103900.0, 24122078.0, "GSM4724529 r1", "0:50", "A:329983157;C:268788282;G:289794374;T:316858580;N:679507", 50, null, null, null, 329983157, 268788282, 289794374, 316858580, 679507, "SRX8931582", "SRS7187990", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94221, null, 0.09615, null, 0.69077, null, 0.47405, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [60615, "SRR12435886", "SRX8931581", "SRS7187989", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 2", "GSM4724528", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 2", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:24 hpf|genotype:ctcf  / ", "GSM4724528", "GSM4724528: RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 2; Danio rerio; RNA Seq", "GSM4724528", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_ctcf_rep2_1.fq.gz", "fastq", 2823674750.0, 56473495.0, "GSM4724528 r1", "0:50", "A:743759446;C:653943934;G:679405104;T:746566266;N:0", 50, null, null, null, 743759446, 653943934, 679405104, 746566266, 0, "SRX8931581", "SRS7187989", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95027, null, 0.08763, null, 0.6984, null, 0.487, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [60616, "SRR12435885", "SRX8931580", "SRS7187988", "SRP277167", "PRJNA656771", "CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]", "GSE156094", "Transcriptome Analysis", "CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator  as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs  which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos  its in vitro removal has only modest effects over gene expression  challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However  the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here  we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes  among them many developmental genes. In addition  we show that chromatin accessibility  both at CTCF sites and at developmental cis regulatory elements CREs  is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution  we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes  leading to altered gene expression patterns during development. Therefore  our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development  providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants  at developmental stages 24 hpf and 48 hpf  with and without xxx of tp53 morpholino", "parent bioproject:PRJNA656767", "pubmed:34518536", null, "RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 1", "GSM4724527", null, "tissue:whole embryo|developmental stage:24 hpf|genotype:ctcf  / ", "RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 1", "Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene", "whole embryo", "Injection of tp53 morpholino was performed at 1 cell stage", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were grown at 28\u00b0C in E3 medium until desired developmental stage", "developmental stage:24 hpf|genotype:ctcf  / ", "GSM4724527", "GSM4724527: RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 1; Danio rerio; RNA Seq", "GSM4724527", null, "1", "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "GEO Accession:GSM4724527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP277167", null, null, "RNAseq_24h_ctcf_rep1_1.fq.gz", "fastq", 2408631250.0, 48172625.0, "GSM4724527 r1", "0:50", "A:623761639;C:570722378;G:584932664;T:629214569;N:0", 50, null, null, null, 623761639, 570722378, 584932664, 629214569, 0, "SRX8931580", "SRS7187988", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95366, null, 0.07765, null, 0.70023, null, 0.47375, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2020-08-12", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [61503, "SRR12780056", "SRX9249644", "SRS7482118", "SRP286526", "PRJNA667677", "Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish", "GSE159087", "Transcriptome Analysis", "Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf  embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ  in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.", null, null, null, "phf tMO 4.7h", "GSM4819005", null, "tissue:embryos|strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "phf tMO 4.7h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al.  nature method  2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples", "embryos", "Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Embryos were cultured in the holfretor water.", "strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "GSM4819005", "GSM4819005: phf tMO 4.7h; Danio rerio; RNA Seq", "GSM4819005", null, "1", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4819005", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP286526", null, null, "phf_tMO_4.7h.fq.gz", "fastq", 1169147800.0, 23382956.0, "GSM4819005 r1", "0:50", "A:311605612;C:272452820;G:269040332;T:316049036;N:0", 50, null, null, null, 311605612, 272452820, 269040332, 316049036, 0, "SRX9249644", "SRS7482118", "SRA1139165", "GEO", "Haitao Li, School of medicine, Tsinghua University", 1, 0.94966, null, 0.07252, null, 0.73651, null, 0.49931, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [61504, "SRR12780055", "SRX9249643", "SRS7482117", "SRP286526", "PRJNA667677", "Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish", "GSE159087", "Transcriptome Analysis", "Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf  embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ  in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.", null, null, null, "std MO 4.7h", "GSM4819004", null, "tissue:embryos|strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "std MO 4.7h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al.  nature method  2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples", "embryos", "Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "Embryos were cultured in the holfretor water.", "strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos", "GSM4819004", "GSM4819004: std MO 4.7h; Danio rerio; RNA Seq", "GSM4819004", null, "1", "Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4819004", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP286526", null, null, "std_MO_4.7h.fq.gz", "fastq", 1169210150.0, 23384203.0, "GSM4819004 r1", "0:50", "A:311848924;C:271805947;G:268541126;T:317014153;N:0", 50, null, null, null, 311848924, 271805947, 268541126, 317014153, 0, "SRX9249643", "SRS7482117", "SRA1139165", "GEO", "Haitao Li, School of medicine, Tsinghua University", 1, 0.94838, null, 0.07833, null, 0.74192, null, 0.48213, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-06", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68473, "SRR17793192", "SRX13955361", "SRS11795776", "SRP357103", "PRJNA801348", "Global studies of Nur77 on metabolism of zebrafish", "PRJNA801348", "Other", "We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique  and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways.", null, null, null, null, "WT3", null, "strain:WT replicate 3|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 6 dpf larvea", "Li lab Nur77 6", "Li lab Nur77 6", "There are two groups: WT and Nur77 mutant. Every group has three replicates.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP357103", null, null, "WT3.fq.gz", "fastq", 1076798350.0, 21535967.0, "WT3.fq.gz", "0:50 1:0", "A:290308649;C:238961327;G:249860004;T:297257553;N:410817", 50, 0, null, null, 290308649, 238961327, 249860004, 297257553, 410817, "SRX13955361", "SRS11795776", "SRA1363249", "Xiamen University|School of pharmaceutical sciences", "Xiamen University", 1, 0.9388, null, 0.12749, null, 0.66087, null, 0.4989, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-27", "Larval", "Larval", "Undetermined", "Undetermined"], [68474, "SRR17793193", "SRX13955360", "SRS11795775", "SRP357103", "PRJNA801348", "Global studies of Nur77 on metabolism of zebrafish", "PRJNA801348", "Other", "We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique  and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways.", null, null, null, null, "WT2", null, "strain:WT replicate 2|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 6 dpf larvea", "Li lab Nur77 5", "Li lab Nur77 5", "There are two groups: WT and Nur77 mutant. Every group has three replicates.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP357103", null, null, "WT2.fq.gz", "fastq", 1076181450.0, 21523629.0, "WT2.fq.gz", "0:50 1:0", "A:289932885;C:238687076;G:249724577;T:297412345;N:424567", 50, 0, null, null, 289932885, 238687076, 249724577, 297412345, 424567, "SRX13955360", "SRS11795775", "SRA1363249", "Xiamen University|School of pharmaceutical sciences", "Xiamen University", 1, 0.93932, null, 0.1297, null, 0.66038, null, 0.48203, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-27", "Larval", "Larval", "Undetermined", "Undetermined"], [68475, "SRR17793194", "SRX13955359", "SRS11795774", "SRP357103", "PRJNA801348", "Global studies of Nur77 on metabolism of zebrafish", "PRJNA801348", "Other", "We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique  and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways.", null, null, null, null, "WT1", null, "strain:WT replicate 1|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 6 dpf larvea", "Li lab Nur77 4", "Li lab Nur77 4", "There are two groups: WT and Nur77 mutant. Every group has three replicates.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP357103", null, null, "WT1.fq.gz", "fastq", 1076191400.0, 21523828.0, "WT1.fq.gz", "0:50 1:0", "A:291276889;C:238480546;G:249179972;T:296814696;N:439297", 50, 0, null, null, 291276889, 238480546, 249179972, 296814696, 439297, "SRX13955359", "SRS11795774", "SRA1363249", "Xiamen University|School of pharmaceutical sciences", "Xiamen University", 1, 0.93825, null, 0.12843, null, 0.66119, null, 0.49668, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-27", "Larval", "Larval", "Undetermined", "Undetermined"], [68476, "SRR17793195", "SRX13955358", "SRS11795773", "SRP357103", "PRJNA801348", "Global studies of Nur77 on metabolism of zebrafish", "PRJNA801348", "Other", "We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique  and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways.", null, null, null, null, "nur77KO3", null, "strain:nur77KO replicate 3|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 6 dpf larvea", "Li lab Nur77 3", "Li lab Nur77 3", "There are two groups: WT and Nur77 mutant. Every group has three replicates.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP357103", null, null, "Nur773.fq.gz", "fastq", 1076004450.0, 21520089.0, "Nur773.fq.gz", "0:50 1:0", "A:290229363;C:238956151;G:246664664;T:299742511;N:411761", 50, 0, null, null, 290229363, 238956151, 246664664, 299742511, 411761, "SRX13955358", "SRS11795773", "SRA1363249", "Xiamen University|School of pharmaceutical sciences", "Xiamen University", 1, 0.93696, null, 0.13828, null, 0.66397, null, 0.48777, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-27", "Larval", "Larval", "Undetermined", "Undetermined"], [68477, "SRR17793196", "SRX13955357", "SRS11795772", "SRP357103", "PRJNA801348", "Global studies of Nur77 on metabolism of zebrafish", "PRJNA801348", "Other", "We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique  and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways.", null, null, null, null, "nur77KO2", null, "strain:nur77KO replicate 2|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 6 dpf larvea", "Li lab Nur77 2", "Li lab Nur77 2", "There are two groups: WT and Nur77 mutant. Every group has three replicates.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP357103", null, null, "Nur772.fq.gz", "fastq", 1075868050.0, 21517361.0, "Nur772.fq.gz", "0:50 1:0", "A:288260097;C:241294246;G:250714084;T:295165628;N:433995", 50, 0, null, null, 288260097, 241294246, 250714084, 295165628, 433995, "SRX13955357", "SRS11795772", "SRA1363249", "Xiamen University|School of pharmaceutical sciences", "Xiamen University", 1, 0.94112, null, 0.11813, null, 0.66582, null, 0.48643, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-27", "Larval", "Larval", "Undetermined", "Undetermined"], [68478, "SRR17793197", "SRX13955356", "SRS11795771", "SRP357103", "PRJNA801348", "Global studies of Nur77 on metabolism of zebrafish", "PRJNA801348", "Other", "We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique  and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways.", null, null, null, null, "nur77KO1", null, "strain:nur77KO replicate 1|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 6 dpf larvea", "Li lab Nur77 1", "Li lab Nur77 1", "There are two groups: WT and Nur77 mutant. Every group has three replicates.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP357103", null, null, "Nur771.fq.gz", "fastq", 1075810450.0, 21516209.0, "Nur771.fq.gz", "0:50 1:0", "A:287851992;C:241486200;G:251500529;T:294560911;N:410818", 50, 0, null, null, 287851992, 241486200, 251500529, 294560911, 410818, "SRX13955356", "SRS11795771", "SRA1363249", "Xiamen University|School of pharmaceutical sciences", "Xiamen University", 1, 0.94193, null, 0.11554, null, 0.6676, null, 0.49728, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-01-27", "Larval", "Larval", "Undetermined", "Undetermined"], [71312, "SRR21487520", "SRX17491012", "SRS15043328", "SRP396256", "PRJNA878480", "Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development", "GSE212929", "Transcriptome Analysis", "To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA  we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function.  We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf  or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.", null, "pubmed:36493774", null, "zebrafish early embryos  WGA treated  5 hpf  dome like stage", "GSM6562796", null, "source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage", "zebrafish early embryos  WGA treated  5 hpf  dome like stage", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", "1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage", "GSM6562796", "GSM6562796: zebrafish early embryos  WGA treated  5 hpf  dome like stage; Danio rerio; RNA Seq", "GSM6562796 r1", "GSM6562796", "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP396256", null, null, "WGA_5h.fq.gz", "fastq", 1059386400.0, 21187728.0, "GSM6562796 r1", "0:50 1:0", "A:277040646;C:250203561;G:245816009;T:285209577;N:1116607", 50, 0, null, null, 277040646, 250203561, 245816009, 285209577, 1116607, "SRX17491012", "SRS15043328", "SRA1496611", "School of life science, Tsinghua University", "School of life science, Tsinghua University", 1, 0.94419, null, 0.03669, null, 0.74919, null, 0.48293, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-09-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [71313, "SRR21487521", "SRX17491011", "SRS15043327", "SRP396256", "PRJNA878480", "Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development", "GSE212929", "Transcriptome Analysis", "To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA  we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function.  We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf  or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.", null, "pubmed:36493774", null, "zebrafish early embryos  WGA treated  4.3 hpf", "GSM6562795", null, "source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage", "zebrafish early embryos  WGA treated  4.3 hpf", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", "1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage", "GSM6562795", "GSM6562795: zebrafish early embryos  WGA treated  4.3 hpf; Danio rerio; RNA Seq", "GSM6562795 r1", "GSM6562795", "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP396256", null, null, "WGA_4.3h.fq.gz", "fastq", 1062790650.0, 21255813.0, "GSM6562795 r1", "0:50 1:0", "A:277911032;C:251212426;G:246864055;T:285783146;N:1019991", 50, 0, null, null, 277911032, 251212426, 246864055, 285783146, 1019991, "SRX17491011", "SRS15043327", "SRA1496611", "School of life science, Tsinghua University", "School of life science, Tsinghua University", 1, 0.94436, null, 0.0365, null, 0.7488, null, 0.47923, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-09-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [71314, "SRR21487522", "SRX17491010", "SRS15043326", "SRP396256", "PRJNA878480", "Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development", "GSE212929", "Transcriptome Analysis", "To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA  we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function.  We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf  or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.", null, "pubmed:36493774", null, "zebrafish early embryos  wildtype  4.3 hpf  dome stage", "GSM6562794", null, "source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:N/A", "zebrafish early embryos  wildtype  4.3 hpf  dome stage", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", "1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:N/A", "GSM6562794", "GSM6562794: zebrafish early embryos  wildtype  4.3 hpf  dome stage; Danio rerio; RNA Seq", "GSM6562794 r1", "GSM6562794", "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP396256", null, null, "WT_4.3h.fq.gz", "fastq", 1063999350.0, 21279987.0, "GSM6562794 r1", "0:50 1:0", "A:280657534;C:249334239;G:244705183;T:288194607;N:1107787", 50, 0, null, null, 280657534, 249334239, 244705183, 288194607, 1107787, "SRX17491010", "SRS15043326", "SRA1496611", "School of life science, Tsinghua University", "School of life science, Tsinghua University", 1, 0.94283, null, 0.06247, null, 0.73474, null, 0.49113, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-09-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74613, "SRR23868264", "SRX19680348", "SRS17049789", "SRP427394", "PRJNA944944", "Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish", "GSE227389", "Transcriptome Analysis", "The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish  based on RNA seq data and some of these genes were validated by qRT\u2013PCR.Further  the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries  mRNA profiles of adult  zebrafish were generated by deep sequencing. Every sample was compose of three  adult individuals.", null, "pubmed:38242380", null, "testes", "GSM7099751", null, "source name:testis|tissue:testis|genotype:WT|geo loc name:missing|collection date:missing", "testes", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz10 whole genome using HISAT  mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.", "testis", null, "Testes and ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", null, "tissue:testis|genotype:WT", "GSM7099751", "GSM7099751: testes; Danio rerio; RNA Seq", "GSM7099751 r1", "GSM7099751", "1", "Testes and ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP427394", null, null, "WT-testis.fq.gz", "fastq", 1176068400.0, 23521368.0, "GSM7099751 r1", "0:50", "A:323799672;C:262049848;G:273563529;T:316045968;N:609383", 50, null, null, null, 323799672, 262049848, 273563529, 316045968, 609383, "SRX19680348", "SRS17049789", "SRA1687194", "Wuhan university", "Wuhan university", 1, 0.93023, null, 0.11308, null, 0.6462, null, 0.49784, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-15", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [74614, "SRR23868265", "SRX19680347", "SRS17049788", "SRP427394", "PRJNA944944", "Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish", "GSE227389", "Transcriptome Analysis", "The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish  based on RNA seq data and some of these genes were validated by qRT\u2013PCR.Further  the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries  mRNA profiles of adult  zebrafish were generated by deep sequencing. Every sample was compose of three  adult individuals.", null, "pubmed:38242380", null, "ovaries", "GSM7099752", null, "source name:ovary|tissue:ovary|genotype:WT|geo loc name:missing|collection date:missing", "ovaries", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz10 whole genome using HISAT  mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.", "ovary", null, "Testes and ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", null, "tissue:ovary|genotype:WT", "GSM7099752", "GSM7099752: ovaries; Danio rerio; RNA Seq", "GSM7099752 r1", "GSM7099752", "1", "Testes and ovaries were isolated  frozen on dry ice  and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP427394", null, null, "WT-ovary.fq.gz", "fastq", 1176463600.0, 23529272.0, "GSM7099752 r1", "0:50", "A:311869864;C:270650722;G:289863261;T:303489229;N:590524", 50, null, null, null, 311869864, 270650722, 289863261, 303489229, 590524, "SRX19680347", "SRS17049788", "SRA1687194", "Wuhan university", "Wuhan university", 1, 0.93488, null, 0.02755, null, 0.75601, null, 0.46986, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-15", "Undetermined", "Undetermined", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 69, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"experiment.platform\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "cDNA", "p2": "BGISEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&experiment.platform=BGISEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&experiment.platform=BGISEQ&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": 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