run_metadata
2 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "Surface Structure"
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 33615 | 33615 | SRR30272850 | SRX25733949 | SRS22373737 | SRP526812 | PRJNA1148907 | Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio | PRJNA1148907 | Other | The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS | pubmed:39947082 | PFOS S2 | Sample2 | strain:Tgins:GFP zebrafish on an AB wildtype background|age:72 hpf|dev stage:protruding mouth stage|collection date:2023 01 03|geo loc name:USA: Massachusetts|sex:NA|tissue:whole body cells|treatment:PFOS 16 uM|BioSampleModel:Model organism or animal | PFOS | PFOS | PFOS | PFOS S2 scRNAseq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PCR | PAIRED | ILLUMINA | NextSeq 500 | SRP526812 | G194-S2-PFOS_S2_L001_R1_001.fastq.gz G194-S2-PFOS_S2_L001_R2_001.fastq.gz G194-S2-PFOS_S2_L002_R1_001.fastq.gz G194-S2-PFOS_S2_L002_R2_001.fastq.gz G194-S2-PFOS_S2_L003_R1_001.fastq.gz G194-S2-PFOS_S2_L003_R2_001.fastq.gz G194-S2-PFOS_S2_L004_R1_001.fastq.gz G194-S2-PFOS_S2_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq | 21751958340.0 | 184338630.0 | G194 S2 PFOS S2 L001 R1 001.fastq.gz | 0:28 1:90 | A:6239773453;C:4634671870;G:5196638658;T:5672561386;N:8312973 | 28 | 90 | 6239773453 | 4634671870 | 5196638658 | 5672561386 | 8312973 | SRX25733949 | SRS22373737 | SRA1949185 | University of Massachusetts Amherst|Environmental Health Sciences | University of Massachusetts Amherst | 2 | 0.01021 | 0.92344 | 0.00451 | 0.22962 | 0.99328 | 0.79847 | 0.28896 | 0.51751 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_generic | generic-scrnaseq-only | United States | 2024-08-16 | Larval | Larval | Trunk | Surface Structure | |||||||||||||||||||
| 33616 | 33616 | SRR30272851 | SRX25733948 | SRS22373736 | SRP526812 | PRJNA1148907 | Single cell RNA sequencing to uncover tissue specific transcriptomic changes induced by perfluorooctanesulfonic acid PFOS in larval zebrafish Danio rerio | PRJNA1148907 | Other | The aim is to to apply single cell RNA sequencing of zebrafish larvae to identify novel tissue specific mechanisms and processes following embryonic exposure to perfluorooctanesulfonic acid PFOS | pubmed:39947082 | DMSO S1 | Sample1 | strain:Tgins:GFP zebrafish on an AB wildtype background|age:72 hpf|dev stage:protruding mouth stage|collection date:2023 01 03|geo loc name:USA: Massachusetts|sex:NA|tissue:whole body cells|treatment:DMSO 0.01%|BioSampleModel:Model organism or animal | DMSO | DMSO | DMSO | DMSO S1 scRNAseq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PCR | PAIRED | ILLUMINA | NextSeq 500 | SRP526812 | G194-S1-DMSO_S1_L001_R1_001.fastq.gz G194-S1-DMSO_S1_L001_R2_001.fastq.gz G194-S1-DMSO_S1_L002_R1_001.fastq.gz G194-S1-DMSO_S1_L002_R2_001.fastq.gz G194-S1-DMSO_S1_L003_R1_001.fastq.gz G194-S1-DMSO_S1_L003_R2_001.fastq.gz G194-S1-DMSO_S1_L004_R1_001.fastq.gz G194-S1-DMSO_S1_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq | 21636838838.0 | 183363041.0 | G194 S1 DMSO S1 L001 R1 001.fastq.gz | 0:28 1:90 | A:6175214014;C:4647929260;G:5248646646;T:5556827078;N:8221840 | 28 | 90 | 6175214014 | 4647929260 | 5248646646 | 5556827078 | 8221840 | SRX25733948 | SRS22373736 | SRA1949185 | University of Massachusetts Amherst|Environmental Health Sciences | University of Massachusetts Amherst | 2 | 0.01048 | 0.92488 | 0.00455 | 0.20966 | 0.99358 | 0.81464 | 0.28056 | 0.57876 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_generic | generic-scrnaseq-only | United States | 2024-08-16 | Larval | Larval | Trunk | Surface Structure |
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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");;