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run_metadata

6 rows where experiment.library_selection = "cDNA", technology = "bulk" and tissue_curation_coarse = "Embryo Imprecise"

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tissue_curation_coarse 1

  • Embryo Imprecise · 6 ✖

tissue_curation 1

technology 1

  • bulk · 6 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 6 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 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
59089 59089 SRR11590436 SRX8157791 SRS6519805 SRP257942 PRJNA627467 Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis GSE149152 Transcriptome Analysis Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run   pubmed:34330825   Low Fli1+ rep2 GSM4491074   tissue:Low Fli1+|cell population:Low Fli1+|genotype:Tgfli1:EGFP Low Fli1+ rep2 Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file Low Fli1+   100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.   cell population:Low Fli1+|genotype:Tgfli1:EGFP GSM4491074 GSM4491074: Low Fli1+ rep2; Danio rerio; RNA Seq GSM4491074   1 100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA. GEO Accession:GSM4491074 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP257942     CI5758_GGCTAC_L005_R1_001.fastq.gz CI5758_GGCTAC_L005_R2_001.fastq.gz fastq fastq 9251096400.0 46255482.0 GSM4491074 r1 0:100 1:100 A:1769289964;C:2789674423;G:2860116416;T:1825482073;N:6533524 100 100     1769289964 2789674423 2860116416 1825482073 6533524 SRX8157791 SRS6519805 SRA1068019 GEO University of Edinburgh 2 0.90817 0.91357 0.12465 0.1278 0.77717 0.78376 0.75104 0.7256 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2020-04-22 Undetermined Embryo Undetermined Embryo Imprecise
59090 59090 SRR11590435 SRX8157790 SRS6519799 SRP257942 PRJNA627467 Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis GSE149152 Transcriptome Analysis Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run   pubmed:34330825   Low Fli1+ rep1 GSM4491073   tissue:Low Fli1+|cell population:Low Fli1+|genotype:Tgfli1:EGFP Low Fli1+ rep1 Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file Low Fli1+   100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.   cell population:Low Fli1+|genotype:Tgfli1:EGFP GSM4491073 GSM4491073: Low Fli1+ rep1; Danio rerio; RNA Seq GSM4491073   1 100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA. GEO Accession:GSM4491073 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP257942     CI5703_CAGATC_L005_R1_001.fastq.gz CI5703_CAGATC_L005_R2_001.fastq.gz fastq fastq 6814746200.0 34073731.0 GSM4491073 r1 0:100 1:100 A:1332637473;C:2025204245;G:2079298693;T:1372597674;N:5008115 100 100     1332637473 2025204245 2079298693 1372597674 5008115 SRX8157790 SRS6519799 SRA1068019 GEO University of Edinburgh 2 0.88252 0.88837 0.1449 0.1472 0.77839 0.78291 0.71852 0.68399 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2020-04-22 Undetermined Embryo Undetermined Embryo Imprecise
59091 59091 SRR11590434 SRX8157789 SRS6519800 SRP257942 PRJNA627467 Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis GSE149152 Transcriptome Analysis Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run   pubmed:34330825   Fli1 rep2 GSM4491072   tissue:Fli1 |cell population:Fli1 |genotype:Tgfli1:EGFP Fli1 rep2 Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file Fli1   100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.   cell population:Fli1 |genotype:Tgfli1:EGFP GSM4491072 GSM4491072: Fli1 rep2; Danio rerio; RNA Seq GSM4491072   1 100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA. GEO Accession:GSM4491072 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP257942     CI5757_TAGCTT_L005_R1_001.fastq.gz CI5757_TAGCTT_L005_R2_001.fastq.gz fastq fastq 8455897000.0 42279485.0 GSM4491072 r1 0:100 1:100 A:1612223258;C:2555349390;G:2614157473;T:1667931765;N:6235114 100 100     1612223258 2555349390 2614157473 1667931765 6235114 SRX8157789 SRS6519800 SRA1068019 GEO University of Edinburgh 2 0.94331 0.94696 0.11995 0.12207 0.76075 0.76796 0.74158 0.71821 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2020-04-22 Undetermined Embryo Undetermined Embryo Imprecise
59092 59092 SRR11590433 SRX8157788 SRS6519797 SRP257942 PRJNA627467 Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis GSE149152 Transcriptome Analysis Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run   pubmed:34330825   Fli1 rep1 GSM4491071   tissue:Fli1 |cell population:Fli1 |genotype:Tgfli1:EGFP Fli1 rep1 Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file Fli1   100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.   cell population:Fli1 |genotype:Tgfli1:EGFP GSM4491071 GSM4491071: Fli1 rep1; Danio rerio; RNA Seq GSM4491071   1 100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA. GEO Accession:GSM4491071 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP257942     CI5701_GCCAAT_L005_R1_001.fastq.gz CI5701_GCCAAT_L005_R2_001.fastq.gz fastq fastq 7474115600.0 37370578.0 GSM4491071 r1 0:100 1:100 A:1480688513;C:2199814780;G:2256979094;T:1531256742;N:5376471 100 100     1480688513 2199814780 2256979094 1531256742 5376471 SRX8157788 SRS6519797 SRA1068019 GEO University of Edinburgh 2 0.93558 0.94034 0.13594 0.13917 0.75118 0.75684 0.66654 0.68344 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2020-04-22 Undetermined Embryo Undetermined Embryo Imprecise
59093 59093 SRR11590438 SRX8157787 SRS6519798 SRP257942 PRJNA627467 Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis GSE149152 Transcriptome Analysis Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run   pubmed:34330825   High Fli1+ rep2 GSM4491076   tissue:High Fli1+|cell population:High Fli1+|genotype:Tgfli1:EGFP High Fli1+ rep2 Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file High Fli1+   100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.   cell population:High Fli1+|genotype:Tgfli1:EGFP GSM4491076 GSM4491076: High Fli1+ rep2; Danio rerio; RNA Seq GSM4491076   1 100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA. GEO Accession:GSM4491076 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP257942     CI5759_CTTGTA_L005_R1_001.fastq.gz CI5759_CTTGTA_L005_R2_001.fastq.gz fastq fastq 6877313200.0 34386566.0 GSM4491076 r1 0:100 1:100 A:1171923636;C:2222996793;G:2262044883;T:1215116923;N:5230965 100 100     1171923636 2222996793 2262044883 1215116923 5230965 SRX8157787 SRS6519798 SRA1068019 GEO University of Edinburgh 2 0.95139 0.95705 0.08927 0.09017 0.81312 0.82004 0.77768 0.75585 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2020-04-22 Undetermined Embryo Undetermined Embryo Imprecise
59094 59094 SRR11590437 SRX8157786 SRS6519796 SRP257942 PRJNA627467 Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis GSE149152 Transcriptome Analysis Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run   pubmed:34330825   High Fli1+ rep1 GSM4491075   tissue:High Fli1+|cell population:High Fli1+|genotype:Tgfli1:EGFP High Fli1+ rep1 Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file High Fli1+   100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.   cell population:High Fli1+|genotype:Tgfli1:EGFP GSM4491075 GSM4491075: High Fli1+ rep1; Danio rerio; RNA Seq GSM4491075   1 100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA. GEO Accession:GSM4491075 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP257942     CI5705_ACTTGA_L005_R1_001.fastq.gz CI5705_ACTTGA_L005_R2_001.fastq.gz fastq fastq 8541050000.0 42705250.0 GSM4491075 r1 0:100 1:100 A:1667536155;C:2542273851;G:2600174460;T:1724878449;N:6187085 100 100     1667536155 2542273851 2600174460 1724878449 6187085 SRX8157786 SRS6519796 SRA1068019 GEO University of Edinburgh 2 0.92757 0.93319 0.14438 0.14609 0.78867 0.79346 0.72736 0.71784 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United Kingdom 2020-04-22 Undetermined Embryo Undetermined Embryo Imprecise

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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");;