run_metadata
4 rows where experiment.library_layout = "SINGLE", experiment.platform = "BGISEQ" and tissue_curation_coarse = "Reproductive System"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48812 | 48812 | SRR7341816 | SRX4215318 | SRS3417596 | SRP150521 | PRJNA476105 | Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary | GSE115806 | Transcriptome Analysis | The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing. | pubmed:30588557 | KO mix | GSM3190267 | source name:Ovary|strain:AB|tissue:Ovary|age:Adult | KO mix | Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. | Ovary | Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | strain:AB|tissue:Ovary|age:Adult | GSM3190267 | GSM3190267: KO mix; Danio rerio; RNA Seq | GSM3190267 | 1 | Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | GEO Accession:GSM3190267 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP150521 | KO-ovary.fq.gz | fastq | 1173123100.0 | 23462462.0 | GSM3190267 r1 | 0:50 1:0 | A:308426188;C:271468505;G:292019086;T:300532126;N:677195 | 50 | 0 | 308426188 | 271468505 | 292019086 | 300532126 | 677195 | SRX4215318 | SRS3417596 | SRA721702 | GEO | Wuhan university | 1 | 0.93261 | 0.02261 | 0.76132 | 0.4585 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2018-06-14 | Adult | Adult | Gonad | Reproductive System | ||||||||||||||||||
| 48813 | 48813 | SRR7341815 | SRX4215317 | SRS3417595 | SRP150521 | PRJNA476105 | Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary | GSE115806 | Transcriptome Analysis | The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing. | pubmed:30588557 | WT mix | GSM3190266 | source name:Ovary|strain:AB|tissue:Ovary|age:Adult | WT mix | Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. | Ovary | Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | strain:AB|tissue:Ovary|age:Adult | GSM3190266 | GSM3190266: WT mix; Danio rerio; RNA Seq | GSM3190266 | 1 | Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | GEO Accession:GSM3190266 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP150521 | WT-ovary.fq.gz | fastq | 1176463600.0 | 23529272.0 | GSM3190266 r1 | 0:50 1:0 | A:311869864;C:270650722;G:289863261;T:303489229;N:590524 | 50 | 0 | 311869864 | 270650722 | 289863261 | 303489229 | 590524 | SRX4215317 | SRS3417595 | SRA721702 | GEO | Wuhan university | 1 | 0.93489 | 0.02765 | 0.75627 | 0.46875 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2018-06-14 | Adult | Adult | Gonad | Reproductive System | ||||||||||||||||||
| 74613 | 74613 | SRR23868264 | SRX19680348 | SRS17049789 | SRP427394 | PRJNA944944 | Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish | GSE227389 | Transcriptome Analysis | The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish based on RNA seq data and some of these genes were validated by qRT–PCR.Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries mRNA profiles of adult zebrafish were generated by deep sequencing. Every sample was compose of three adult individuals. | pubmed:38242380 | testes | GSM7099751 | source name:testis|tissue:testis|genotype:WT|geo loc name:missing|collection date:missing | testes | Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. | testis | Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | tissue:testis|genotype:WT | GSM7099751 | GSM7099751: testes; Danio rerio; RNA Seq | GSM7099751 r1 | GSM7099751 | 1 | Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP427394 | WT-testis.fq.gz | fastq | 1176068400.0 | 23521368.0 | GSM7099751 r1 | 0:50 | A:323799672;C:262049848;G:273563529;T:316045968;N:609383 | 50 | 323799672 | 262049848 | 273563529 | 316045968 | 609383 | SRX19680348 | SRS17049789 | SRA1687194 | Wuhan university | Wuhan university | 1 | 0.93023 | 0.11308 | 0.6462 | 0.49784 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-03-15 | Undetermined | Undetermined | Gonad | Reproductive System | |||||||||||||||||||
| 74614 | 74614 | SRR23868265 | SRX19680347 | SRS17049788 | SRP427394 | PRJNA944944 | Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish | GSE227389 | Transcriptome Analysis | The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish based on RNA seq data and some of these genes were validated by qRT–PCR.Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries mRNA profiles of adult zebrafish were generated by deep sequencing. Every sample was compose of three adult individuals. | pubmed:38242380 | ovaries | GSM7099752 | source name:ovary|tissue:ovary|genotype:WT|geo loc name:missing|collection date:missing | ovaries | Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. | ovary | Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | tissue:ovary|genotype:WT | GSM7099752 | GSM7099752: ovaries; Danio rerio; RNA Seq | GSM7099752 r1 | GSM7099752 | 1 | Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP427394 | WT-ovary.fq.gz | fastq | 1176463600.0 | 23529272.0 | GSM7099752 r1 | 0:50 | A:311869864;C:270650722;G:289863261;T:303489229;N:590524 | 50 | 311869864 | 270650722 | 289863261 | 303489229 | 590524 | SRX19680347 | SRS17049788 | SRA1687194 | Wuhan university | Wuhan university | 1 | 0.93488 | 0.02755 | 0.75601 | 0.46986 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-03-15 | Undetermined | Undetermined | Gonad | Reproductive 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");;