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
48305,SRR10368285,SRX7076279,SRS5592164,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,sa37 16hpf 2,GSM4144779,,source name:whole embryo|tissue:whole embryo|age:16 hpf sa37,sa37 16hpf 2,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:16 hpf sa37,GSM4144779,GSM4144779: sa37 16hpf 2; Danio rerio; RNA Seq,GSM4144779,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM4144779,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,S04.fastq.gz,fastq,2166354993.0,28701604.0,GSM4144779 r1,0:75.48 1:0,A:566482594;C:525711117;G:579970160;T:493751194;N:439928,75,0,,,566482594,525711117,579970160,493751194,439928,SRX7076279,SRS5592164,SRA703389,GEO,Kanazawa University,1,0.92378,,0.09905,,0.74479,,0.52368,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2019-10-30,Segmentation,Embryo,Whole Organism,All anatomical structures
48306,SRR10368284,SRX7076278,SRS5592163,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,sa37 12hpf 2,GSM4144778,,source name:whole embryo|tissue:whole embryo|age:12 hpf sa37,sa37 12hpf 2,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:12 hpf sa37,GSM4144778,GSM4144778: sa37 12hpf 2; Danio rerio; RNA Seq,GSM4144778,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM4144778,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,S03.fastq.gz,fastq,1653073372.0,21903605.0,GSM4144778 r1,0:75.47 1:0,A:433206792;C:402537379;G:446761303;T:370161548;N:406350,75,0,,,433206792,402537379,446761303,370161548,406350,SRX7076278,SRS5592163,SRA703389,GEO,Kanazawa University,1,0.91778,,0.12219,,0.76684,,0.54487,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2019-10-30,Segmentation,Embryo,Whole Organism,All anatomical structures
48307,SRR10368283,SRX7076277,SRS5592162,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,WT 16hpf 2,GSM4144777,,source name:whole embryo|tissue:whole embryo|age:16 hpf type,WT 16hpf 2,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:16 hpf type,GSM4144777,GSM4144777: WT 16hpf 2; Danio rerio; RNA Seq,GSM4144777,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM4144777,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,S02.fastq.gz,fastq,2178611783.0,28900952.0,GSM4144777 r1,0:75.38 1:0,A:566689783;C:530433539;G:590611812;T:488215395;N:2661254,75,0,,,566689783,530433539,590611812,488215395,2661254,SRX7076277,SRS5592162,SRA703389,GEO,Kanazawa University,1,0.93637,,0.10293,,0.7542,,0.53437,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2019-10-30,Segmentation,Embryo,Whole Organism,All anatomical structures
48308,SRR10368282,SRX7076276,SRS5592161,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,WT 12hpf 2,GSM4144776,,source name:whole embryo|tissue:whole embryo|age:12 hpf type,WT 12hpf 2,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:12 hpf type,GSM4144776,GSM4144776: WT 12hpf 2; Danio rerio; RNA Seq,GSM4144776,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker  which includes the three nucleotide barcodes  followed by 3? linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM4144776,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,S01.fastq.gz,fastq,2235469804.0,29611055.0,GSM4144776 r1,0:75.49 1:0,A:582276989;C:546056334;G:609905170;T:497018748;N:212563,75,0,,,582276989,546056334,609905170,497018748,212563,SRX7076276,SRS5592161,SRA703389,GEO,Kanazawa University,1,0.9362,,0.12401,,0.76857,,0.48408,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2019-10-30,Segmentation,Embryo,Whole Organism,All anatomical structures
48309,SRR7162665,SRX4080963,SRS3298238,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,sa37 16hpf,GSM3141418,,source name:whole embryo|tissue:whole embryo|age:16 hpf sa37,sa37 16hpf,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:16 hpf sa37,GSM3141418,GSM3141418: sa37 16hpf; Danio rerio; RNA Seq,GSM3141418,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM3141418,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,KB4.fastq.gz,fastq,1534816794.0,20351965.0,GSM3141418 r1,0:75.41 1:0,A:406883394;C:371384442;G:408553824;T:347148313;N:846821,75,0,,,406883394,371384442,408553824,347148313,846821,SRX4080963,SRS3298238,SRA703389,GEO,Kanazawa University,1,0.90303,,0.11364,,0.7726,,0.54943,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2018-05-14,Segmentation,Embryo,Whole Organism,All anatomical structures
48310,SRR7162664,SRX4080962,SRS3298237,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,sa37 12hpf,GSM3141417,,source name:whole embryo|tissue:whole embryo|age:12 hpf sa37,sa37 12hpf,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:12 hpf sa37,GSM3141417,GSM3141417: sa37 12hpf; Danio rerio; RNA Seq,GSM3141417,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM3141417,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,KB3.fastq.gz,fastq,1102623174.0,14620872.0,GSM3141417 r1,0:75.41 1:0,A:294837961;C:265832591;G:295010626;T:246478308;N:463688,75,0,,,294837961,265832591,295010626,246478308,463688,SRX4080962,SRS3298237,SRA703389,GEO,Kanazawa University,1,0.89407,,0.145,,0.79299,,0.58846,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2018-05-14,Segmentation,Embryo,Whole Organism,All anatomical structures
48311,SRR7162663,SRX4080961,SRS3298236,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,WT 16hpf,GSM3141416,,source name:whole embryo|tissue:whole embryo|age:16 hpf type,WT 16hpf,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:16 hpf type,GSM3141416,GSM3141416: WT 16hpf; Danio rerio; RNA Seq,GSM3141416,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM3141416,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,KB2.fastq.gz,fastq,1436366901.0,19049708.0,GSM3141416 r1,0:75.40 1:0,A:385845952;C:344690132;G:380040548;T:324881238;N:909031,75,0,,,385845952,344690132,380040548,324881238,909031,SRX4080961,SRS3298236,SRA703389,GEO,Kanazawa University,1,0.90003,,0.11916,,0.77579,,0.54897,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2018-05-14,Segmentation,Embryo,Whole Organism,All anatomical structures
48312,SRR7162662,SRX4080960,SRS3298235,SRP145615,PRJNA471311,Gene expression analysis of jam3b mutant embryos,GSE114416,Transcriptome Analysis,Junctional adhesion molecule 3 Jam3 is a cell adhesion molecule that is involved in cell cell interaction  cell migration  and cell polarization in many tissue including the epithelium  endothelium  and hematopoietic cells. Although Jam3 is functionally relevant for both hematopoietic and vascular endothelial cells  the role of Jam3 in hematopoietic or vascular development is still unknown. In this study  a zebrafish jam3b mutant line  jam3b sa37  was used for the cap analysis gene expression CAGE sequencing to identify genes that are involved in hematopoietic and/or vascular development in the zebrafish embryo. Overall design: Whole embryos mRNA profiles of wild type or jam3b sa37 embryos at 12 or 16 hpf were generated by CAGE sequencing using Illumina NextSeq500.,,,,WT 12hpf,GSM3141415,,source name:whole embryo|tissue:whole embryo|age:12 hpf type,WT 12hpf,Illumina RTA software was used for base calling. Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio danRer10 using the Burrows Wheeler Aligner BWA and HiSAT2 software. Tags per million TPM were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5. Genome build: danRer10 Supplementary files format and content: Tab delimited text files include tags per million TPM values for each sample.,whole embryo,,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,,tissue:whole embryo|age:12 hpf type,GSM3141415,GSM3141415: WT 12hpf; Danio rerio; RNA Seq,GSM3141415,,1,Total RNAs were extracted from staged embryos using RNeasy Mini Kit QIAGEN. 2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit DNAFORM. five primecaps of RNAs are biotinylated post reverse transcription. RNA cDNA hybirds were then captured by streptavidin conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker  which includes the three nucleotide barcodes  followed by 3′ linker ligation. Second strand synthesis was performed using the nAnT iCAGE second primer  creating the final double stranded DNA product. Cap analysis gene expression CAGE sequencing,GEO Accession:GSM3141415,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP145615,,,KB1.fastq.gz,fastq,1207735359.0,16013304.0,GSM3141415 r1,0:75.42 1:0,A:319723192;C:291608829;G:328515002;T:267246909;N:641427,75,0,,,319723192,291608829,328515002,267246909,641427,SRX4080960,SRS3298235,SRA703389,GEO,Kanazawa University,1,0.90112,,0.14655,,0.79762,,0.52207,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cage,unknown,bulk,unknown,unknown,,Japan,2018-05-14,Segmentation,Embryo,Whole Organism,All anatomical structures
55266,SRR10418684,SRX7116713,SRS5465204,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S06 Prim5,,strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  Prim 5  stage  Cycloheximide treated for 2 hours,Prim5 tagCAGE CHX,Prim5 tagCAGE CHX,Tagging CAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP223930,,,S06_Prim5_tagCAGE-CHX.fastq.gz,fastq,272077515.0,10076945.0,S06 Prim5 tagCAGE CHX.fastq.gz,0:27,A:67002738;C:62164745;G:73707100;T:69202932;N:0,27,,,,67002738,62164745,73707100,69202932,0,SRX7116713,SRS5465204,SRA993027,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.44237,,0.05018,,0.80296,,0.84125,,27,,B,,usable mapping rate,illumina,early_illumina,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-08,Pharyngula,Embryo,Whole Organism,All anatomical structures
55267,SRR10418685,SRX7116712,SRS5465204,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S06 Prim5,,strain:AB|dev stage:Prim 5|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  Prim 5  stage  DMSO control,Prim5 tagCAGE DMSO,Prim5 tagCAGE DMSO,Tagging CAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP223930,,,S06_Prim5_tagCAGE-DMSO.fastq.gz,fastq,339322419.0,12567497.0,S06 Prim5 tagCAGE DMSO.fastq.gz,0:27,A:81884992;C:78138597;G:89012923;T:90285907;N:0,27,,,,81884992,78138597,89012923,90285907,0,SRX7116712,SRS5465204,SRA993027,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.43876,,0.05032,,0.82404,,0.85765,,27,,B,,usable mapping rate,illumina,early_illumina,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-08,Pharyngula,Embryo,Whole Organism,All anatomical structures
55269,SRR10215485,SRX6935170,SRS5465205,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S07 LongPec,,strain:AB|dev stage:Long pec|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo   Long pec stage,LongPec nAnTiCAGE,LongPec nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,NextSeq 500,,SRP223930,,,S07_LongPec_nAnTiCAGE.fastq.gz,fastq,1326115656.0,18418273.0,S07 LongPec nAnTiCAGE.fastq.gz,0:72 1:0,A:355337919;C:317217156;G:362577018;T:290983563;N:0,72,0,,,355337919,317217156,362577018,290983563,0,SRX6935170,SRS5465205,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.94675,,0.13499,,0.77512,,0.56663,,72,,B,,usable mapping rate,illumina,nextseq,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Hatching,Embryo,Whole Organism,All anatomical structures
55272,SRR10215488,SRX6935167,SRS5465202,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S04 30Epi,,strain:AB|dev stage:zfs:0000015|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  zfs:0000015 stage,zfs:0000015 nAnTiCAGE,zfs:0000015 nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S04_30pEpib_nAnTiCAGE.fastq.gz,fastq,629440272.0,13113339.0,S04 30pEpib nAnTiCAGE.fastq.gz,0:48 1:0,A:170201862;C:150343558;G:166046900;T:141987430;N:860522,48,0,,,170201862,150343558,166046900,141987430,860522,SRX6935167,SRS5465202,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.83843,,0.15935,,0.81499,,0.71304,,48,,B,,usable mapping rate,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Blastula,Embryo,Whole Organism,All anatomical structures
55273,SRR10215489,SRX6935166,SRS5465201,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S03 512Cells,,strain:AB|dev stage:512 cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  512 cell stage,512Cells nAnTiCAGE,512Cells nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S03_512Cells_nAnTiCAGE.fastq.gz,fastq,725783040.0,15120480.0,S03 512Cells nAnTiCAGE.fastq.gz,0:48 1:0,A:196224130;C:171017037;G:189882541;T:167660445;N:998887,48,0,,,196224130,171017037,189882541,167660445,998887,SRX6935166,SRS5465201,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.85441,,0.14832,,0.79659,,0.68016,,48,,B,,usable mapping rate,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Blastula,Embryo,Whole Organism,All anatomical structures
55274,SRR10215490,SRX6935165,SRS5465200,SRP223930,PRJNA575342,CAGE /CappedRNA sequencig,PRJNA575342,Other,CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development,,,,,S02 128Cells,,strain:AB|dev stage:128 cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq of Danio rerio  whole embryo  128 cell stage,128Cells nAnTiCAGE,128Cells nAnTiCAGE,nAnTiCAGE,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP223930,,,S02_128Cells_nAnTiCAGE.fastq.gz,fastq,510549408.0,10636446.0,S02 128Cells nAnTiCAGE.fastq.gz,0:48 1:0,A:135389960;C:121538362;G:140642547;T:112273195;N:705344,48,0,,,135389960,121538362,140642547,112273195,705344,SRX6935165,SRS5465200,SRA971223,University of Birmingham|Cancer and Genomic Sciences,University of Birmingham,1,0.84843,,0.14523,,0.79845,,0.68592,,48,,B,,usable mapping rate,illumina,hiseq_era,full_length,cage,unknown,bulk,unknown,unknown,,United Kingdom,2019-10-02,Blastula,Embryo,Whole Organism,All anatomical structures
69378,SRR18516702,SRX14647801,SRS12413210,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007475BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Whole cell CAGE,DCD003740SQ,DCD003740SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003740SQ.USERdanio-user.R1.fastq.gz,fastq,57981552.0,1207949.0,CAGE seq Mueller lab 0013AS.DCD003740SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:13228227;C:15492921;G:15505739;T:13750626;N:4039,48,0,,,13228227,15492921,15505739,13750626,4039,SRX14647801,SRS12413210,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.18388,,0.02619,,0.85811,,0.52264,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69379,SRR18516703,SRX14647800,SRS12413216,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007476BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Nuclear CAGE,DCD003719SQ,DCD003719SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003719SQ.USERdanio-user.R1.fastq.gz,fastq,585510192.0,12198129.0,CAGE seq Mueller lab 0014AS.DCD003719SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:129885703;C:153766182;G:160138903;T:141666883;N:52521,48,0,,,129885703,153766182,160138903,141666883,52521,SRX14647800,SRS12413216,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.20391,,0.04196,,0.83453,,0.4979,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69380,SRR18516704,SRX14647799,SRS12413216,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007476BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Nuclear CAGE,DCD003718SQ,DCD003718SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003718SQ.USERdanio-user.R1.fastq.gz,fastq,593136528.0,12357011.0,CAGE seq Mueller lab 0014AS.DCD003718SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:130366174;C:156810351;G:159219365;T:146691922;N:48716,48,0,,,130366174,156810351,159219365,146691922,48716,SRX14647799,SRS12413216,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.14873,,0.03239,,0.86557,,0.49634,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69381,SRR18516705,SRX14647798,SRS12413216,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007476BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Nuclear CAGE,DCD003723SQ,DCD003723SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003723SQ.USERdanio-user.R1.fastq.gz,fastq,422696256.0,8806172.0,CAGE seq Mueller lab 0014AS.DCD003723SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:92712632;C:111696999;G:115145846;T:103105611;N:35168,48,0,,,92712632,111696999,115145846,103105611,35168,SRX14647798,SRS12413216,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.1594,,0.02997,,0.85591,,0.48496,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69382,SRR18516706,SRX14647797,SRS12413215,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007477BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Nuclear CAGE,DCD003737SQ,DCD003737SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003737SQ.USERdanio-user.R1.fastq.gz,fastq,1041108672.0,21689764.0,CAGE seq Mueller lab 0014AS.DCD003737SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:233996885;C:276232291;G:275987771;T:254800016;N:91709,48,0,,,233996885,276232291,275987771,254800016,91709,SRX14647797,SRS12413215,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.19665,,0.0423,,0.84271,,0.49525,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69383,SRR18516707,SRX14647796,SRS12413215,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007477BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Nuclear CAGE,DCD003729SQ,DCD003729SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003729SQ.USERdanio-user.R1.fastq.gz,fastq,383268528.0,7984761.0,CAGE seq Mueller lab 0014AS.DCD003729SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:83789437;C:103371728;G:102876480;T:93198236;N:32647,48,0,,,83789437,103371728,102876480,93198236,32647,SRX14647796,SRS12413215,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.15605,,0.03059,,0.86951,,0.50369,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69384,SRR18516708,SRX14647795,SRS12413215,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007477BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Nuclear CAGE,DCD003734SQ,DCD003734SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003734SQ.USERdanio-user.R1.fastq.gz,fastq,560665392.0,11680529.0,CAGE seq Mueller lab 0014AS.DCD003734SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:123278501;C:149059346;G:152514412;T:135763704;N:49429,48,0,,,123278501,149059346,152514412,135763704,49429,SRX14647795,SRS12413215,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.16518,,0.02906,,0.85283,,0.47924,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69385,SRR18516709,SRX14647794,SRS12413214,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007471BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Whole cell CAGE,DCD003731SQ,DCD003731SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003731SQ.USERdanio-user.R1.fastq.gz,fastq,534745104.0,11140523.0,CAGE seq Mueller lab 0013AS.DCD003731SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:122900964;C:145291239;G:142314928;T:124199394;N:38579,48,0,,,122900964,145291239,142314928,124199394,38579,SRX14647794,SRS12413214,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.21193,,0.03662,,0.8576,,0.51061,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69386,SRR18516710,SRX14647793,SRS12413214,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007471BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Whole cell CAGE,DCD003733SQ,DCD003733SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003733SQ.USERdanio-user.R1.fastq.gz,fastq,1106623152.0,23054649.0,CAGE seq Mueller lab 0013AS.DCD003733SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:244437769;C:302018709;G:293780395;T:266329857;N:56422,48,0,,,244437769,302018709,293780395,266329857,56422,SRX14647793,SRS12413214,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.25973,,0.02959,,0.84778,,0.50948,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69387,SRR18516711,SRX14647792,SRS12413214,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007471BS,,strain:WT|age:42hpf|dev stage:High pec|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq High pec Whole cell CAGE,DCD003735SQ,DCD003735SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003735SQ.USERdanio-user.R1.fastq.gz,fastq,829987920.0,17291415.0,CAGE seq Mueller lab 0013AS.DCD003735SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:189638839;C:226118233;G:218991435;T:195178858;N:60555,48,0,,,189638839,226118233,218991435,195178858,60555,SRX14647792,SRS12413214,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.20953,,0.03562,,0.85285,,0.52927,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69388,SRR18516712,SRX14647791,SRS12413213,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007472BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Whole cell CAGE,DCD003730SQ,DCD003730SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003730SQ.USERdanio-user.R1.fastq.gz,fastq,358730736.0,7473557.0,CAGE seq Mueller lab 0013AS.DCD003730SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:82114871;C:96481695;G:97889447;T:82217691;N:27032,48,0,,,82114871,96481695,97889447,82217691,27032,SRX14647791,SRS12413213,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.22955,,0.03488,,0.84719,,0.51204,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69389,SRR18516713,SRX14647790,SRS12413209,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007478BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Nuclear CAGE,DCD003732SQ,DCD003732SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003732SQ.USERdanio-user.R1.fastq.gz,fastq,833831760.0,17371495.0,CAGE seq Mueller lab 0014AS.DCD003732SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:184529953;C:221676233;G:220734592;T:206820467;N:70515,48,0,,,184529953,221676233,220734592,206820467,70515,SRX14647790,SRS12413209,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.16336,,0.03655,,0.88633,,0.47894,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69390,SRR18516714,SRX14647789,SRS12413213,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007472BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Whole cell CAGE,DCD003738SQ,DCD003738SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003738SQ.USERdanio-user.R1.fastq.gz,fastq,1160622288.0,24179631.0,CAGE seq Mueller lab 0013AS.DCD003738SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:261568282;C:313737609;G:310169539;T:275088632;N:58226,48,0,,,261568282,313737609,310169539,275088632,58226,SRX14647789,SRS12413213,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.27025,,0.0344,,0.86505,,0.50961,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69391,SRR18516715,SRX14647788,SRS12413213,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007472BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Whole cell CAGE,DCD003722SQ,DCD003722SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003722SQ.USERdanio-user.R1.fastq.gz,fastq,666656256.0,13888672.0,CAGE seq Mueller lab 0013AS.DCD003722SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:149770159;C:178068662;G:177661463;T:161122864;N:33108,48,0,,,149770159,178068662,177661463,161122864,33108,SRX14647788,SRS12413213,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.25511,,0.02671,,0.86436,,0.50531,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69392,SRR18516716,SRX14647787,SRS12413212,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007473BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Whole cell CAGE,DCD003727SQ,DCD003727SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003727SQ.USERdanio-user.R1.fastq.gz,fastq,924879888.0,19268331.0,CAGE seq Mueller lab 0013AS.DCD003727SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:214005056;C:251321459;G:244648845;T:214835794;N:68734,48,0,,,214005056,251321459,244648845,214835794,68734,SRX14647787,SRS12413212,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.2165,,0.03701,,0.84768,,0.54102,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69393,SRR18516717,SRX14647786,SRS12413212,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007473BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Whole cell CAGE,DCD003717SQ,DCD003717SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003717SQ.USERdanio-user.R1.fastq.gz,fastq,1485845376.0,30955112.0,CAGE seq Mueller lab 0013AS.DCD003717SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:329122121;C:402514173;G:390388645;T:363745867;N:74570,48,0,,,329122121,402514173,390388645,363745867,74570,SRX14647786,SRS12413212,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.23893,,0.0248,,0.86125,,0.50849,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69394,SRR18516718,SRX14647785,SRS12413212,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007473BS,,strain:WT|age:24hpf|dev stage:Prim 5|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq Prim Whole cell CAGE,DCD003739SQ,DCD003739SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003739SQ.USERdanio-user.R1.fastq.gz,fastq,1372622736.0,28596307.0,CAGE seq Mueller lab 0013AS.DCD003739SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:306709302;C:373224967;G:360990874;T:331626639;N:70954,48,0,,,306709302,373224967,360990874,331626639,70954,SRX14647785,SRS12413212,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.26574,,0.02914,,0.85113,,0.52147,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
69395,SRR18516719,SRX14647784,SRS12413211,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007474BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Nuclear CAGE,DCD003721SQ,DCD003721SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003721SQ.USERdanio-user.R1.fastq.gz,fastq,425483904.0,8864248.0,CAGE seq Mueller lab 0014AS.DCD003721SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:98642418;C:114264552;G:114112965;T:98433833;N:30136,48,0,,,98642418,114264552,114112965,98433833,30136,SRX14647784,SRS12413211,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.21658,,0.03797,,0.85226,,0.48604,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69396,SRR18516720,SRX14647783,SRS12413211,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007474BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Nuclear CAGE,DCD003736SQ,DCD003736SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003736SQ.USERdanio-user.R1.fastq.gz,fastq,533681088.0,11118356.0,CAGE seq Mueller lab 0014AS.DCD003736SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:115850766;C:142773032;G:143794343;T:131220159;N:42788,48,0,,,115850766,142773032,143794343,131220159,42788,SRX14647783,SRS12413211,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.15054,,0.0279,,0.87434,,0.4867,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69397,SRR18516721,SRX14647782,SRS12413211,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007474BS,,strain:WT|age:14hpf|dev stage:5 9 somites|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq 5 9 somites Nuclear CAGE,DCD003726SQ,DCD003726SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003726SQ.USERdanio-user.R1.fastq.gz,fastq,250307520.0,5214740.0,CAGE seq Mueller lab 0014AS.DCD003726SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:55705158;C:65429159;G:68119770;T:61031856;N:21577,48,0,,,55705158,65429159,68119770,61031856,21577,SRX14647782,SRS12413211,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.19864,,0.04157,,0.85279,,0.48786,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
69398,SRR18516722,SRX14647781,SRS12413210,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007475BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Whole cell CAGE,DCD003720SQ,DCD003720SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003720SQ.USERdanio-user.R1.fastq.gz,fastq,536292432.0,11172759.0,CAGE seq Mueller lab 0013AS.DCD003720SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:122756671;C:142850582;G:140364671;T:130293257;N:27251,48,0,,,122756671,142850582,140364671,130293257,27251,SRX14647781,SRS12413210,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.23072,,0.04674,,0.89572,,0.59187,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69399,SRR18516723,SRX14647780,SRS12413210,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007475BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Whole cell CAGE,DCD003725SQ,DCD003725SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0013AS.DCD003725SQ.USERdanio-user.R1.fastq.gz,fastq,1839979776.0,38332912.0,CAGE seq Mueller lab 0013AS.DCD003725SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:422772310;C:484519947;G:479159876;T:453437875;N:89768,48,0,,,422772310,484519947,479159876,453437875,89768,SRX14647780,SRS12413210,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.22646,,0.03978,,0.88574,,0.556,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69400,SRR18516724,SRX14647779,SRS12413209,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007478BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Nuclear CAGE,DCD003728SQ,DCD003728SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003728SQ.USERdanio-user.R1.fastq.gz,fastq,778510272.0,16218964.0,CAGE seq Mueller lab 0014AS.DCD003728SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:170505572;C:207531743;G:206655879;T:193751108;N:65970,48,0,,,170505572,207531743,206655879,193751108,65970,SRX14647779,SRS12413209,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.1419,,0.02783,,0.8954,,0.49693,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures
69401,SRR18516725,SRX14647778,SRS12413209,SRP366491,PRJNA821088,Enhancer calling in early stages,PRJNA821088,Other,CAGE seq for enhancer calling in early stages for the DANIO CODE project.,,,,,DCD007478BS,,strain:WT|age:4.7hpf|dev stage:zfs:0000015|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,CAGE seq zfs:0000015 Nuclear CAGE,DCD003724SQ,DCD003724SQ,max read length:50,,,RNA-Seq,TRANSCRIPTOMIC,CAGE,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP366491,,,CAGE-seq_Mueller_lab_0014AS.DCD003724SQ.USERdanio-user.R1.fastq.gz,fastq,641108496.0,13356427.0,CAGE seq Mueller lab 0014AS.DCD003724SQ.USERdanio user.R1.fastq.gz,0:48 1:0,A:143927298;C:167543966;G:171107575;T:158473503;N:56154,48,0,,,143927298,167543966,171107575,158473503,56154,SRX14647778,SRS12413209,SRA1393740,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.20203,,0.0454,,0.87091,,0.51364,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,cage,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Blastula,Embryo,Embryo Imprecise,All anatomical structures