run_metadata
2 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "bulk"
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 64387 | 64387 | SRR14679149 | SRX11017526 | SRS9089834 | SRP321802 | PRJNA733247 | Danio rerio breed:Danio Raw sequence reads | PRJNA733247 | Whole Genome Sequencing | zebrafish muscle tissue for scRNA seq and bulk RNA seq | Model organism or animal sample from Danio rerio | zebrafish | breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal | scRNA seq | runx2b / scRNA seq | runx2b / scRNA seq | tail muscle without xxx bone | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP321802 | MU_S2_L003_R1_001.fastq.gz MU_S2_L003_R2_001.fastq.gz | fastq fastq | 112565768100.0 | 375219227.0 | MU S2 L003 R1 001.fastq.gz | 0:150 1:150 | A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410 | 150 | 150 | 34329910863 | 17430450121 | 18090145246 | 42713500460 | 1761410 | SRX11017526 | SRS9089834 | SRA1238123 | Huazhong Agricultural university|Huazhong Agricultural university | Huazhong Agricultural university | 2 | 0.34692 | 0.92476 | 0.05138 | 0.09375 | 0.98543 | 0.82371 | 0.68433 | 0.7376 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | bulk | bulk | China | 2021-05-29 | Juvenile | Juvenile | Muscle | Muscular System | ||||||||||||||||||||
| 64388 | 64388 | SRR14679150 | SRX11017525 | SRS9089834 | SRP321802 | PRJNA733247 | Danio rerio breed:Danio Raw sequence reads | PRJNA733247 | Whole Genome Sequencing | zebrafish muscle tissue for scRNA seq and bulk RNA seq | Model organism or animal sample from Danio rerio | zebrafish | breed:Danio|dev stage:60 day|sex:missing|tissue:muscle|BioSampleModel:Model organism or animal | scRNA seq | runx2b+/+ scRNA seq | runx2b+/+ scRNA seq | tail muscle with intermuscular bone | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP321802 | WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz | fastq fastq | 99838157100.0 | 332793857.0 | WT S1 L003 R1 001.fastq.gz | 0:150 1:150 | A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720 | 150 | 150 | 30283010374 | 15529232903 | 16181518775 | 37842782328 | 1612720 | SRX11017525 | SRS9089834 | SRA1238123 | Huazhong Agricultural university|Huazhong Agricultural university | Huazhong Agricultural university | 2 | 0.34302 | 0.92611 | 0.04637 | 0.09453 | 0.98701 | 0.83658 | 0.71917 | 0.76074 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | bulk | bulk | China | 2021-05-29 | Juvenile | Juvenile | Muscle | Muscular 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");;