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38 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "CAGE" and experiment.library_strategy = "RNA-Seq"

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devstage_curation 4

tissue_curation 2

tissue_curation_coarse 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 38 ✖

experiment.library_source 1

experiment.library_selection 1

  • CAGE · 38 ✖

experiment.library_layout 1

  • SINGLE · 38 ✖

devstage_curation_coarse 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
48305 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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