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run_metadata

4 rows where experiment.library_strategy = "ChIP-Seq" and tissue_curation_coarse = "Hematopoietic System"

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tissue_curation_coarse 1

  • Hematopoietic System · 4 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • ChIP-Seq · 4 ✖

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
71666 71666 SRR21912675 SRX17898597 SRS15415408 SRP402754 PRJNA890767 Input of Setdb1 ChIP seq PRJNA890767 Other           Input of Setdb1 ChIP seq 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal                 Input of Setdb1 ChIP seq Input of Setdb1 ChIP seq 2 Input of Setdb1 ChIP seq 2 Input of Setdb1 ChIP seq of replicate 2     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402754     Input of Setdb1 ChIP seq_2_R1.fastq.gz Input of Setdb1 ChIP seq_2_R2.fastq.gz fastq fastq 10384123200.0 34613744.0 Input of Setdb1 ChIP seq 2 R1.fastq.gz 0:150 1:150 A:2881450025;C:2101684440;G:2781250994;T:2619703377;N:34364 150 150     2881450025 2101684440 2781250994 2619703377 34364 SRX17898597 SRS15415408 SRA1520925 East China Normal University|School of Life Sciences East China Normal University 2 0.85089 0.8531 0.74147 0.74359 0.72295 0.72243 0.49118 0.48923 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic System
71667 71667 SRR21912676 SRX17898596 SRS15415407 SRP402754 PRJNA890767 Input of Setdb1 ChIP seq PRJNA890767 Other           Input of Setdb1 ChIP seq 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal                 Input of Setdb1 ChIP seq Input of Setdb1 ChIP seq 1 Input of Setdb1 ChIP seq 1 Input of Setdb1 ChIP seq of replicate 1     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402754     Input of Setdb1 ChIP seq_1_R1.fastq.gz Input of Setdb1 ChIP seq_1_R2.fastq.gz fastq fastq 12920086500.0 43066955.0 Input of Setdb1 ChIP seq 1 R1.fastq.gz 0:150 1:150 A:3743886319;C:2621020407;G:3091990806;T:3463122519;N:66449 150 150     3743886319 2621020407 3091990806 3463122519 66449 SRX17898596 SRS15415407 SRA1520925 East China Normal University|School of Life Sciences East China Normal University 2 0.84709 0.84605 0.73727 0.73696 0.71622 0.71825 0.49278 0.49029 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic System
71668 71668 SRR21913250 SRX17899172 SRS15415910 SRP402767 PRJNA890871 Setdb1 ChIP seq PRJNA890871 Other           Setdb1 ChIP seq 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal                 Setdb1 ChIP seq Setdb1 ChIP seq 2 Setdb1 ChIP seq 2 Setdb1 ChIP seq of replicate 2     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402767     Setdb1 ChIP seq_2_R1.fastq.gz Setdb1 ChIP seq_2_R2.fastq.gz fastq fastq 12909692700.0 43032309.0 Setdb1 ChIP seq 2 R1.fastq.gz 0:150 1:150 A:3496408461;C:2593261434;G:3585073580;T:3234906241;N:42984 150 150     3496408461 2593261434 3585073580 3234906241 42984 SRX17899172 SRS15415910 SRA1520950 East China Normal University|School of Life Sciences East China Normal University 2 0.80561 0.80471 0.69212 0.69176 0.71924 0.71999 0.49445 0.4953 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic System
71669 71669 SRR21913251 SRX17899171 SRS15415909 SRP402767 PRJNA890871 Setdb1 ChIP seq PRJNA890871 Other           Setdb1 ChIP seq 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal                 Setdb1 ChIP seq Setdb1 ChIP seq 1 Setdb1 ChIP seq 1 Setdb1 ChIP seq of replicate 1     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402767     Setdb1 ChIP seq_1_R1.fastq.gz Setdb1 ChIP seq_1_R2.fastq.gz fastq fastq 9908302200.0 33027674.0 Setdb1 ChIP seq 1 R1.fastq.gz 0:150 1:150 A:2799788817;C:2060083633;G:2416457009;T:2631940230;N:32511 150 150     2799788817 2060083633 2416457009 2631940230 32511 SRX17899171 SRS15415909 SRA1520950 East China Normal University|School of Life Sciences East China Normal University 2 0.7718 0.77187 0.66177 0.66128 0.72088 0.71963 0.49562 0.49458 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic 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");;