run_metadata
2 rows where experiment.library_selection = "RT-PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Cell Line"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 61655 | 61655 | SRR12903379 | SRX9368290 | SRS7590200 | SRP288657 | PRJNA672138 | RNA seq of zebrafish HSCs of cftr mutant at 48hpf | PRJNA672138 | Other | To reveal the role of cftr in HSC of zebrafish embryo at 48hpf | cmyb+GFP HSC | cmyb+GFP HSC | strain:AB|isolate:FACS|breed:Egg water|age:0.8year|dev stage:48hpf|sex:not applicable|tissue:HSC|cell line:HSC|cell type:HSC|collected by:FACS|BioSampleModel:Model organism or animal | RNA Seq of cftr mutant cmyb+GFP HSC | 2 | 2 | cftr mutant cmyb+GFP HSC | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP288657 | CF-HSC_L4_Q803604.R1.fastq.gz CF-HSC_L4_Q803604.R2.fastq.gz | fastq fastq | 9923396100.0 | 33077987.0 | CF HSC L4 Q803604.R1.fastq.gz | 0:150 1:150 | A:2814592323;C:2140796492;G:2161622902;T:2806345512;N:38871 | 150 | 150 | 2814592323 | 2140796492 | 2161622902 | 2806345512 | 38871 | SRX9368290 | SRS7590200 | SRA1148101 | Sichuan University|West China Second University Hospital | Sichuan University | 2 | 0.92974 | 0.93014 | 0.25254 | 0.25232 | 0.739 | 0.73933 | 0.51947 | 0.51997 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | China | 2020-10-26 | Multi-stage | Multi-stage | Cell Line | Cell Line | ||||||||||||||||||||
| 61656 | 61656 | SRR12903380 | SRX9368289 | SRS7590200 | SRP288657 | PRJNA672138 | RNA seq of zebrafish HSCs of cftr mutant at 48hpf | PRJNA672138 | Other | To reveal the role of cftr in HSC of zebrafish embryo at 48hpf | cmyb+GFP HSC | cmyb+GFP HSC | strain:AB|isolate:FACS|breed:Egg water|age:0.8year|dev stage:48hpf|sex:not applicable|tissue:HSC|cell line:HSC|cell type:HSC|collected by:FACS|BioSampleModel:Model organism or animal | RNA Seq of WT cmyb+GFP HSC | 1 | 1 | WT cmyb+GFP HSC | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP288657 | WT-HSC_L4_Q802604.R1.fastq.gz WT-HSC_L4_Q802604.R2.fastq.gz | fastq fastq | 10530660600.0 | 35102202.0 | WT HSC L4 Q802604.R1.fastq.gz | 0:150 1:150 | A:2977953142;C:2283045134;G:2298868821;T:2970751970;N:41533 | 150 | 150 | 2977953142 | 2283045134 | 2298868821 | 2970751970 | 41533 | SRX9368289 | SRS7590200 | SRA1148101 | Sichuan University|West China Second University Hospital | Sichuan University | 2 | 0.93722 | 0.93625 | 0.21368 | 0.21331 | 0.72859 | 0.729 | 0.49389 | 0.49309 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | China | 2020-10-26 | Multi-stage | Multi-stage | Cell Line | Cell Line |
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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");;