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
34966,SRR32588723,SRX27895228,SRS24266230,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from embryo zero hpf,C2 F2 24,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 24 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from embyo 24 hpf,C2 F2 24,C2 F2 24,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m54313U_231109_165320.hifi_reads.flnc.fastq.gz,fastq,7642144881.0,3850910.0,m54313U 231109 165320.hifi reads.flnc.fastq.gz,0:1984.50,A:2137607023;C:1720821414;G:1812220379;T:1971496065;N:0,1984,,,,2137607023,1720821414,1812220379,1971496065,0,SRX27895228,SRS24266230,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Pharyngula,Embryo,Muscle,Muscular System
53013,SRR9662026,SRX6422902,SRS5079692,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Muscle rep2,GSM3934894,,source name:Tissue|strain:Tuebingen|tissue:Muscle,YueLab RNA Seq Muscle rep2,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Muscle,GSM3934894,GSM3934894: YueLab RNA Seq Muscle rep2; Danio rerio; RNA Seq,GSM3934894,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934894,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Muscle-rep2_1.fastq.gz YueLab-RNA-Seq-Muscle-rep2_2.fastq.gz,fastq fastq,2021185692.0,19815546.0,GSM3934894 r1,0:51 1:51,A:508251350;C:473502441;G:462707891;T:537489259;N:39234751,51,51,,,508251350,473502441,462707891,537489259,39234751,SRX6422902,SRS5079692,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.94958,0.95251,0.06157,0.05992,0.77398,0.77802,0.50205,0.53541,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Muscle,Muscular System
53014,SRR9662025,SRX6422901,SRS5079691,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Muscle rep1,GSM3934893,,source name:Tissue|strain:Tuebingen|tissue:Muscle,YueLab RNA Seq Muscle rep1,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Muscle,GSM3934893,GSM3934893: YueLab RNA Seq Muscle rep1; Danio rerio; RNA Seq,GSM3934893,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934893,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Muscle-rep1_1.fastq.gz YueLab-RNA-Seq-Muscle-rep1_2.fastq.gz,fastq fastq,3952674128.0,32728471.0,GSM3934893 r1,0:60.49 1:60.28,A:1031292985;C:933897200;G:906173487;T:1081251504;N:58952,60,60,,,1031292985,933897200,906173487,1081251504,58952,SRX6422901,SRS5079691,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.98113,0.98146,0.05897,0.05792,0.77973,0.78374,0.56016,0.55409,61,60,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Muscle,Muscular System
71456,SRR21631159,SRX17631561,SRS15166364,SRP398129,PRJNA882122,Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish,GSE213728,Transcriptome Analysis,Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100  prepared for stranded Illumina sequencing  and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.,,,,Slow twitch Muscle  tgPACPrdm1a:eGFP  Sample2,GSM6592891,,source name:slow twitch muscle|tissue:slow twitch muscle|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing,Slow twitch Muscle  tgPACPrdm1a:eGFP  Sample2,Read aligment with STAR  counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file,slow twitch muscle,For cyclopamine treated samples  embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf,standard Illumina Kit for stranded RNAseq,Embryos reared at 28C until 24hpf.,tissue:slow twitch muscle|genotype:wildtype|treatment:n1,GSM6592891,GSM6592891: Slow twitch Muscle  tgPACPrdm1a:eGFP  Sample2; Danio rerio; RNA Seq,GSM6592891 r1,GSM6592891,1,standard Illumina Kit for stranded RNAseq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP398129,,loader:fastq load.py,Sample3_GFP_24hpf_S3_L002_R1_001.fastq.gz Sample3_GFP_24hpf_S3_L002_R2_001.fastq.gz,fastq fastq,19887469194.0,65852547.0,GSM6592891 r1,0:151 1:151,A:4595886435;C:4222799298;G:6711875529;T:4353875479;N:3032453,151,151,,,4595886435,4222799298,6711875529,4353875479,3032453,SRX17631561,SRS15166364,SRA1501497,"Lencer Laboratory, Department of Biology, Lafayette College","Lencer Laboratory, Department of Biology, Lafayette College",2,0.92086,0.91566,0.10394,0.10303,0.75808,0.76002,0.51563,0.51331,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2022-09-19,Pharyngula,Embryo,Muscle,Muscular System
71458,SRR21631161,SRX17631559,SRS15166362,SRP398129,PRJNA882122,Mutations in cdon and boc affect trunk neural crest cell migration and slow twitch muscle development in zebrafish,GSE213728,Transcriptome Analysis,Bulk RNA seq of isolated slow twtich muscle and neural crest cells from 24 hpf zebrafish. Overall design: Bulk RNA seq data from FAC sorted slow twitch muscle and neural crest cells isolated from trunks of 24 hpf zebrafish embryos. Trunks of embryos were manually dissected and cells were disassociated using Accumax. Embryos were doubly transgenic for tgsox10:mRFP transgene that labels neural crest cells and tgPACprdm1a:eGFP transgene that labels slow twitch muscle and muscle pioneer cells. Neural crest cells and slow twitch muscle cells were isolated by FACS on a MoFlow XDP100  prepared for stranded Illumina sequencing  and sequenced on a NovaSeq600 PE 150bp. Gene expression summaries were produced using featurecounts subread package and DESeq2.,,,,Slow twitch Muscle  tgPACPrdm1a:eGFP  Sample1,GSM6592889,,source name:slow twitch muscle|tissue:slow twitch muscle|genotype:wildtype|treatment:n1|geo loc name:missing|collection date:missing,Slow twitch Muscle  tgPACPrdm1a:eGFP  Sample1,Read aligment with STAR  counts generated by featurecounts subread. Expression from DESeq2 using normTransform function Supplementary files format and content: tab delim text file Supplementary files format and content: tab delim text file,slow twitch muscle,For cyclopamine treated samples  embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf,standard Illumina Kit for stranded RNAseq,Embryos reared at 28C until 24hpf.,tissue:slow twitch muscle|genotype:wildtype|treatment:n1,GSM6592889,GSM6592889: Slow twitch Muscle  tgPACPrdm1a:eGFP  Sample1; Danio rerio; RNA Seq,GSM6592889 r1,GSM6592889,1,standard Illumina Kit for stranded RNAseq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP398129,,loader:fastq load.py,Sample1_GFP_24hpf_S1_L002_R1_001.fastq.gz Sample1_GFP_24hpf_S1_L002_R2_001.fastq.gz,fastq fastq,19122998172.0,63321186.0,GSM6592889 r1,0:151 1:151,A:4422627777;C:4011278190;G:6496127381;T:4190045039;N:2919785,151,151,,,4422627777,4011278190,6496127381,4190045039,2919785,SRX17631559,SRS15166362,SRA1501497,"Lencer Laboratory, Department of Biology, Lafayette College","Lencer Laboratory, Department of Biology, Lafayette College",2,0.91304,0.90702,0.10612,0.10501,0.77242,0.77415,0.52048,0.51584,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2022-09-19,Pharyngula,Embryo,Muscle,Muscular System