run_metadata
3 rows where devstage_curation = "Zygote" and experiment.library_selection = "CAGE"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36424 | 36424 | SRR516545 | SRX156307 | SRS347187 | SRP013950 | PRJNA169500 | Danio rerio embryonic promoterome | PRJNA169500 | Transcriptome Analysis | Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development. | pubmed:24531765 | Zebrafish wild type AB strain unfertilized egg | D. rerio unfertilized egg | D. rerio unfertilized egg | CAGE D. rerio unfertilized egg | CAGE D. rerio unfertilized egg run2 | D. rerio unfertilized egg | 1 | OTHER | TRANSCRIPTOMIC | CAGE | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP013950 | 115273233.0 | 4269379.0 | CAGE D. rerio unfertilized egg run1 | 0:27 | A:29909511;C:24823784;G:32519899;T:28020039;N:0 | 27 | 29909511 | 24823784 | 32519899 | 28020039 | 0 | SRX156307 | SRS347187 | SRA055273 | University of Bergen | ZEPROME consortium | 1 | 0.49872 | 0.07655 | 0.81673 | 0.80445 | 27 | B | usable mapping rate | illumina | early_illumina | unknown | cage | unknown | bulk | unknown | unknown | Unknown | 2012-06-28 | Zygote | Embryo | Oocyte | Reproductive System | |||||||||||||||||||||||||||
| 36425 | 36425 | SRR516546 | SRX156307 | SRS347187 | SRP013950 | PRJNA169500 | Danio rerio embryonic promoterome | PRJNA169500 | Transcriptome Analysis | Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development. | pubmed:24531765 | Zebrafish wild type AB strain unfertilized egg | D. rerio unfertilized egg | D. rerio unfertilized egg | CAGE D. rerio unfertilized egg | CAGE D. rerio unfertilized egg run2 | D. rerio unfertilized egg | 1 | OTHER | TRANSCRIPTOMIC | CAGE | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP013950 | 112673943.0 | 4173109.0 | CAGE D. rerio unfertilized egg run2 | 0:27 | A:28315221;C:24199098;G:32599482;T:27560142;N:0 | 27 | 28315221 | 24199098 | 32599482 | 27560142 | 0 | SRX156307 | SRS347187 | SRA055273 | University of Bergen | ZEPROME consortium | 1 | 0.46201 | 0.06422 | 0.82118 | 0.82184 | 27 | B | usable mapping rate | illumina | early_illumina | unknown | cage | unknown | bulk | unknown | unknown | Unknown | 2012-06-28 | Zygote | Embryo | Oocyte | Reproductive System | |||||||||||||||||||||||||||
| 55275 | 55275 | SRR10215491 | SRX6935164 | SRS5465199 | SRP223930 | PRJNA575342 | CAGE /CappedRNA sequencig | PRJNA575342 | Other | CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development | S01 1Cell | strain:AB|dev stage:1cell|sex:N/A|tissue:whole embryo|BioSampleModel:Model organism or animal | CAGE seq of Danio rerio whole embryo 1 cell stage | 1Cell nAnTiCAGE | 1Cell nAnTiCAGE | nAnTiCAGE | RNA-Seq | TRANSCRIPTOMIC | CAGE | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP223930 | S01_1Cells_nAnTiCAGE_1.fastq.gz S01_1Cells_nAnTiCAGE_2.fastq.gz | fastq fastq | 1193891117.0 | 6060361.0 | S01 1Cells nAnTiCAGE 1.fastq.gz | 0:97 1:100 | A:286037352;C:298140071;G:310668851;T:297430066;N:1614777 | 97 | 100 | 286037352 | 298140071 | 310668851 | 297430066 | 1614777 | SRX6935164 | SRS5465199 | SRA971223 | University of Birmingham|Cancer and Genomic Sciences | University of Birmingham | 2 | 0.93733 | 0.97059 | 0.08219 | 0.07881 | 0.76682 | 0.75834 | 0.53879 | 0.54537 | 97 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | cage | unknown | bulk | unknown | unknown | United Kingdom | 2019-10-02 | Zygote | Embryo | Whole Organism | All anatomical structures |
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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");;