run_metadata
2 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "other" and tissue_curation_coarse = "Digestive System"
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 52131 | 52131 | SRR8944754 | SRX5724887 | SRS4662952 | SRP193452 | PRJNA534016 | fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome | PRJNA534016 | Other | In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs hepatic and serum lipid content in fabp2 gene knockout KO zebrafish we performed the intestinal transcriptome analysis. | In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs hepatic and serum lipid content in fabp2 gene knockout KO zebrafish we performed the intestinal transcriptome analysis. | fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome | intestinal transcriptome sequencing of fabp2 gene KO and WT zebrafish | isolate:fabp2 gene KO and WT zebrafish|dev stage:adult|sex:not collected|tissue:intestine|collected by:Yan Zhao|collection date:2017 10|geo loc name:China: Wuhan city Hubei province|sample type:tissue sample|BioSampleModel:Model organism or animal | intestinal transcritome sequencing | fabp2 gene KO Danio rerio | fabp2 gene KO Danio rerio | Total RNAs were extracted from the intestine of experimental fish using Trizol. The construction of the cDNA library and sequencing were performed using Illumina NovaSeq 6000 HiSeq 2000 platform Illumina CA USA. | RNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP193452 | KO1_1.fastq.gz KO2_2.fastq.gz KO2_1.fastq.gz KO1_2.fastq.gz | fastq fastq fastq fastq | 21269908500.0 | 70899695.0 | KO1 1.fastq.gz | 0:150 1:150 | A:5602268133;C:4968099632;G:4965298378;T:5733027255;N:1215102 | 150 | 150 | 5602268133 | 4968099632 | 4965298378 | 5733027255 | 1215102 | SRX5724887 | SRS4662952 | SRA878388 | Huazhong Agricultural University|Fisheries College | Huazhong Agricultural University | 2 | 0.92003 | 0.92121 | 0.03272 | 0.03273 | 0.78488 | 0.78859 | 0.49044 | 0.48398 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | other | unknown | bulk | unknown | unknown | China | 2019-04-23 | Adult | Adult | Gut | Digestive System | |||||||||||||||||||
| 52132 | 52132 | SRR8944755 | SRX5724886 | SRS4662952 | SRP193452 | PRJNA534016 | fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome | PRJNA534016 | Other | In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs hepatic and serum lipid content in fabp2 gene knockout KO zebrafish we performed the intestinal transcriptome analysis. | In order to fully reveal the possible molecular mechanisms of varied intestinal n 3 HUAFs hepatic and serum lipid content in fabp2 gene knockout KO zebrafish we performed the intestinal transcriptome analysis. | fabp2 gene knockout KO and wild type WT zebrafish Danio Rerio intestinal transcriptome | intestinal transcriptome sequencing of fabp2 gene KO and WT zebrafish | isolate:fabp2 gene KO and WT zebrafish|dev stage:adult|sex:not collected|tissue:intestine|collected by:Yan Zhao|collection date:2017 10|geo loc name:China: Wuhan city Hubei province|sample type:tissue sample|BioSampleModel:Model organism or animal | intestinal transcritome sequencing | wild type Danio rerio | wild type Danio rerio | Total RNAs were extracted from the intestine of experimental fish using Trizol. The construction of the cDNA library and sequencing were performed using Illumina NovaSeq 6000 HiSeq 2001 platform Illumina CA USA. | RNA-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP193452 | WT1_1.fastq.gz WT1_2.fastq.gz WT2_1.fastq.gz WT2_2.fastq.gz | fastq fastq fastq fastq | 23433575100.0 | 78111917.0 | WT1 1.fastq.gz | 0:150 1:150 | A:6211885445;C:5476158510;G:5474363796;T:6269801731;N:1365618 | 150 | 150 | 6211885445 | 5476158510 | 5474363796 | 6269801731 | 1365618 | SRX5724886 | SRS4662952 | SRA878388 | Huazhong Agricultural University|Fisheries College | Huazhong Agricultural University | 2 | 0.92141 | 0.92214 | 0.04124 | 0.04142 | 0.77664 | 0.78182 | 0.5318 | 0.52116 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | other | unknown | bulk | unknown | unknown | China | 2019-04-23 | Adult | Adult | Gut | Digestive 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");;