run_metadata: 9386
This data as json
| 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 |
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| 9386 | ERR147028 | ERX122956 | ERS151238 | ERP001552 | PRJEB3112 | The effects of temperature on gene expression in zebrafish | E-MTAB-1155 | Transcriptome Analysis | Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C. | Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. | WH3 F M pooled fish | SAMEA1487362 | Genepool | AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487362|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex | The effects of temperature on gene expression in zebrafish | E MTAB 1155:WH3 seq | WH3 pooled extract | The effects of temperature on gene expression in zebrafish | Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. | Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP001552 | Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish | ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 | WH3_1.fq.gz WH3_2.fq.gz | fastq fastq | 3197103894.0 | 15827247.0 | E MTAB 1155:WH3 | 0:101 1:101 | A:829020337;C:767623553;G:780642278;T:818288216;N:1529510 | 101 | 101 | 829020337 | 767623553 | 780642278 | 818288216 | 1529510 | ERX122956 | ERS151238 | ERA142144 | Genepool|Department of Biology, McMaster University | Genepool|Department of Biology, McMaster University | 2 | 0.94791 | 0.91975 | 0.03726 | 0.03735 | 0.84291 | 0.85622 | 0.4972 | 0.50314 | 101 | 101 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | unknown | bulk | unknown | unknown | Canada | 2012-08-21 | Adult | Adult | Whole Organism | All anatomical structures |