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
68254,SRR18327318,SRX14464504,SRS11744581,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow,nanoCAGE zebrafish TU testis rep2,nanoCAGE zebrafish TU testis rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_testis_BR2.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR2.R2.fastq.gz,fastq fastq,2408261400.0,15886644.0,nano TUzfish combined deep testis BR2.R1.fastq.gz,0:75.80 1:75.80,A:589293804;C:562741604;G:604867589;T:650872884;N:485519,75,75,,,589293804,562741604,604867589,650872884,485519,SRX14464504,SRS11744581,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.05991,0.93925,0.00631,0.04834,0.91364,0.67671,0.54402,0.49323,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Gonad,Reproductive System
68255,SRR18327319,SRX14464503,SRS11744582,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis shallow,nanoCAGE zebrafish TU testis rep1,nanoCAGE zebrafish TU testis rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_testis_BR1.R1.fastq.gz nano_TUzfish_combined_deep_testis_BR1.R2.fastq.gz,fastq fastq,2655464100.0,17518322.0,nano TUzfish combined deep testis BR1.R1.fastq.gz,0:75.79 1:75.79,A:648423774;C:624425183;G:667510545;T:714557704;N:546894,75,75,,,648423774,624425183,667510545,714557704,546894,SRX14464503,SRS11744582,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.05205,0.9337,0.00433,0.0458,0.92086,0.68631,0.5426,0.50321,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Gonad,Reproductive System
68256,SRR18327320,SRX14464502,SRS11744580,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow,nanoCAGE zebrafish TU brain rep2,nanoCAGE zebrafish TU brain rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_brain_BR2.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR2.R2.fastq.gz,fastq fastq,2120070300.0,13983927.0,nano TUzfish combined deep brain BR2.R1.fastq.gz,0:75.80 1:75.80,A:521597394;C:502052046;G:539140115;T:556851976;N:428769,75,75,,,521597394,502052046,539140115,556851976,428769,SRX14464502,SRS11744580,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.05946,0.93361,0.00648,0.07284,0.91739,0.70025,0.57506,0.48669,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Brain,Nervous System
68257,SRR18327321,SRX14464501,SRS11744579,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male brain shallow,nanoCAGE zebrafish TU brain rep1,nanoCAGE zebrafish TU brain rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nano_TUzfish_combined_deep_brain_BR1.R1.fastq.gz nano_TUzfish_combined_deep_brain_BR1.R2.fastq.gz,fastq fastq,1958802000.0,12919047.0,nano TUzfish combined deep brain BR1.R1.fastq.gz,0:75.81 1:75.81,A:485271176;C:461368873;G:496521163;T:515247447;N:393341,75,75,,,485271176,461368873,496521163,515247447,393341,SRX14464501,SRS11744579,SRA1385043,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.0666,0.93487,0.00689,0.0747,0.91175,0.70027,0.57062,0.49364,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-03-17,Adult,Adult,Brain,Nervous System
68258,SRR17709722,SRX13872770,SRS11744581,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis,nanoCAGE zebrafish TU testis rep2,nanoCAGE zebrafish TU testis shallow rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_testis_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep2.R2.fastq.gz,fastq fastq,1257997200.0,8218216.0,nanoCAGE zebrafish TU testis rep2.R1.fastq.gz,0:76.54 1:76.54,A:307675653;C:294445668;G:315944501;T:339570175;N:361203,76,76,,,307675653,294445668,315944501,339570175,361203,SRX13872770,SRS11744581,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.06846,0.93772,0.00675,0.04699,0.90293,0.67986,0.52867,0.49221,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Gonad,Reproductive System
68259,SRR17709723,SRX13872769,SRS11744582,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU testis rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult male testis,nanoCAGE zebrafish TU testis rep1,nanoCAGE zebrafish TU testis shallow rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_testis_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_testis_rep1.R2.fastq.gz,fastq fastq,1351312800.0,8823980.0,nanoCAGE zebrafish TU testis rep1.R1.fastq.gz,0:76.57 1:76.57,A:329750139;C:318355694;G:339653380;T:363149300;N:404287,76,76,,,329750139,318355694,339653380,363149300,404287,SRX13872769,SRS11744582,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.06051,0.93247,0.00473,0.0437,0.91088,0.68943,0.52768,0.49868,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Gonad,Reproductive System
68260,SRR17709724,SRX13872768,SRS11744580,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep2,,strain:Tuebingen|isolate:rep2|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult female brain,nanoCAGE zebrafish TU brain rep2,nanoCAGE zebrafish TU brain shallow rep2,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_brain_rep2.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep2.R2.fastq.gz,fastq fastq,1114647450.0,7281108.0,nanoCAGE zebrafish TU brain rep2.R1.fastq.gz,0:76.54 1:76.54,A:273967636;C:264512491;G:283567362;T:292276557;N:323404,76,76,,,273967636,264512491,283567362,292276557,323404,SRX13872768,SRS11744580,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.06736,0.93327,0.00663,0.0712,0.90792,0.70283,0.55337,0.4859,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Brain,Nervous System
68261,SRR17709725,SRX13872767,SRS11744579,SRP356302,PRJNA799647,Epigenomic analysis reveals prevalent contribution of transposable elements to cis regulatory elements  tissue specific expression  and alternative promoters in zebrafish,PRJNA799647,Other,Transposable elements TEs encode regulatory elements that impact gene expression in multiple species  yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here  we systematically investigate the epigenomic and transcriptomic landscape of TEs across eleven adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE derived transcriptional units expressed in a tissue specific manner. Finally  we show that novel TE derived promoters can initiate tissue specific transcription of alternative isoforms. This work provides a 10 comprehensive profile of TE activity across normal zebrafish tissues  shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.,,,,,zebrafish TU brain rep1,,strain:Tuebingen|isolate:rep1|age:6 mpf|dev stage:adult|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,nanoCAGE seq of Danio rerio Tubingen: adult female brain,nanoCAGE zebrafish TU brain rep1,nanoCAGE zebrafish TU brain shallow rep1,nanoCAGE seq with polyA pulldown,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,PAIRED,ILLUMINA,NextSeq 500,,SRP356302,,,nanoCAGE_zebrafish_TU_brain_rep1.R1.fastq.gz nanoCAGE_zebrafish_TU_brain_rep1.R2.fastq.gz,fastq fastq,1040194800.0,6794999.0,nanoCAGE zebrafish TU brain rep1.R1.fastq.gz,0:76.54 1:76.54,A:257427323;C:245563114;G:263853643;T:273054571;N:296149,76,76,,,257427323,245563114,263853643,273054571,296149,SRX13872767,SRS11744579,SRA1360415,Washington University in St. Louis|Department of Genetics,Washington University in St. Louis,2,0.07308,0.93461,0.00714,0.07167,0.9051,0.70199,0.56162,0.48821,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,United States,2022-01-23,Adult,Adult,Brain,Nervous System