run_metadata
1 row where devstage_curation = "Zygote" and tissue_curation = "Liver"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 75608 | 75608 | SRR24742192 | SRX20519420 | SRS17829368 | SRP439656 | PRJNA975724 | Key factors in the process of biliary epithelial cells to bipotential progenitor cells dedifferentiation | PRJNA975724 | Other | Uncover the regulatory mechanisms underlying biliary cell dedifferentiation. | The fish were treated with mtz at 5 dpf and then the livers were collected post 24 hours treatment namly regeneration 0 hour. | scRNA seq of zebrafish R0h livers | Livers of lfabp:Dendra2 NTR fish at mtz R0h | strain:ABGO|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:mtz R0h|sex:pooled male and female|tissue:liver|birth location:China|collection date:2021 04 29|geo loc name:China: Chongqing|BioSampleModel:Model organism or animal | scRNA seq of zebrafish R0h livers | 20210429 S3 R0 | 20210429 S3 R0 | Using Chromium Single cell three prime GEM v3.1 Reagent kit | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP439656 | R21049148-20210429-S3-R0-1_combined_R1.fastq.gz R21049148-20210429-S3-R0-1_combined_R2.fastq.gz R21049148-20210429-S3-R0-2_combined_R1.fastq.gz R21049148-20210429-S3-R0-2_combined_R2.fastq.gz R21049148-20210429-S3-R0-3_combined_R1.fastq.gz R21049148-20210429-S3-R0-3_combined_R2.fastq.gz R21049148-20210429-S3-R0-4_combined_R1.fastq.gz R21049148-20210429-S3-R0-4_combined_R2.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq | 108860887800.0 | 362869626.0 | R21049148 20210429 S3 R0 1 combined R1.fastq.gz | 0:150 1:150 | A:46078842047;C:20145501988;G:19787836142;T:22846772612;N:1935011 | 150 | 150 | 46078842047 | 20145501988 | 19787836142 | 22846772612 | 1935011 | SRX20519420 | SRS17829368 | SRA1643264 | Institute of Developmental Biology and Regenerative Medicine|Southwest University | Institute of Developmental Biology and Regenerative Medicine AccuraMed Company | 2 | 0.0 | 0.92113 | 0.0 | 0.15798 | 1.0 | 0.81215 | 0.58532 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | China | 2023-05-25 | Zygote | Embryo | Liver | Liver and Biliary 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");;