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run_metadata

3 rows where technology = "bulk" and tissue_curation = "Endothelium"

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tissue_curation_coarse 1

tissue_curation 1

  • Endothelium · 3 ✖

technology 1

  • bulk · 3 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

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
59850 59850 SRR12045008 SRX8573978 SRS6865977 SRP267842 PRJNA640350 Bulk RNA seq data to assess an improved zebrafish transcriptome annotation GSE152759 Transcriptome Analysis oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS   pubmed:32831172   Nr2f2andY1 positive rep3 GSM4625929   tissue:venous endothelial cells|Stage:38 hpf isolated cells Nr2f2andY1 positive rep3 Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation venous endothelial cells embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting. total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech   Stage:38 hpf isolated cells GSM4625929 GSM4625929: Nr2f2andY1 positive rep3; Danio rerio; RNA Seq GSM4625929   1 total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech GEO Accession:GSM4625929 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP267842     Nr2f2_y1_WT3.R1.fastq Nr2f2_y1_WT3.R2.fastq fastq fastq 4563696700.0 45636967.0 GSM4625929 r1 0:50 1:50 A:1065004679;C:1130434821;G:1255426694;T:1110932954;N:1897552 50 50     1065004679 1130434821 1255426694 1110932954 1897552 SRX8573978 SRS6865977 SRA1088645 GEO Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School 2 0.82873 0.84247 0.30011 0.31275 0.76952 0.7713 0.70461 0.5211 50 50 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter bulk bulk bulk   United States 2020-06-18 Pharyngula Embryo Endothelium Cardiovascular System
59851 59851 SRR12045007 SRX8573977 SRS6865975 SRP267842 PRJNA640350 Bulk RNA seq data to assess an improved zebrafish transcriptome annotation GSE152759 Transcriptome Analysis oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS   pubmed:32831172   Nr2f2andY1 positive rep2 GSM4625928   tissue:venous endothelial cells|Stage:38 hpf isolated cells Nr2f2andY1 positive rep2 Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation venous endothelial cells embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting. total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech   Stage:38 hpf isolated cells GSM4625928 GSM4625928: Nr2f2andY1 positive rep2; Danio rerio; RNA Seq GSM4625928   1 total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech GEO Accession:GSM4625928 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP267842     Nr2f2_y1_WT2.R1.fastq Nr2f2_y1_WT2.R2.fastq fastq fastq 5035288300.0 50352883.0 GSM4625928 r1 0:50 1:50 A:1193841347;C:1228803073;G:1365132247;T:1245428530;N:2083103 50 50     1193841347 1228803073 1365132247 1245428530 2083103 SRX8573977 SRS6865975 SRA1088645 GEO Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School 2 0.81964 0.83355 0.31676 0.32935 0.77394 0.77179 0.69865 0.54887 50 50 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter bulk bulk bulk   United States 2020-06-18 Pharyngula Embryo Endothelium Cardiovascular System
59852 59852 SRR12045006 SRX8573976 SRS6865974 SRP267842 PRJNA640350 Bulk RNA seq data to assess an improved zebrafish transcriptome annotation GSE152759 Transcriptome Analysis oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS   pubmed:32831172   Nr2f2andY1 positive rep1 GSM4625927   tissue:venous endothelial cells|Stage:38 hpf isolated cells Nr2f2andY1 positive rep1 Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples if index sequences were non redundant we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95 RefSeq GCF 000002035.6 or a custom annotation V4.3.gtf included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation venous endothelial cells embryos were dissociated into single cell suspensions immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting. total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech   Stage:38 hpf isolated cells GSM4625927 GSM4625927: Nr2f2andY1 positive rep1; Danio rerio; RNA Seq GSM4625927   1 total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech GEO Accession:GSM4625927 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP267842     Nr2f2_y1_WT1.R1.fastq Nr2f2_y1_WT1.R2.fastq fastq fastq 4790242000.0 47902420.0 GSM4625927 r1 0:50 1:50 A:1058654389;C:1248085905;G:1387245634;T:1094388168;N:1867904 50 50     1058654389 1248085905 1387245634 1094388168 1867904 SRX8573976 SRS6865974 SRA1088645 GEO Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School 2 0.83369 0.84436 0.23642 0.24601 0.77788 0.77977 0.73738 0.55719 50 50 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter bulk bulk bulk   United States 2020-06-18 Pharyngula Embryo Endothelium Cardiovascular System

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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");;