run_metadata: 40964
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40964 | SRR3470784 | SRX1738397 | SRS1418769 | SRP074244 | PRJNA320266 | Dietary intake influences fertility and offspring development in zebrafish. | GSE81007 | Transcriptome Analysis | We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets. | pubmed:27870856 | 60mg arm 1 | GSM2140603 | source name:Unfertilized eggs|strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg | 60mg arm 1 | Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9 | Unfertilized eggs | Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks. | The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols | Zebrafish were maintained under standard conditions | strain:In house AB/Pet shop|tissue:Unfertilized eggs|FISH age:9 mpf|treatment arm:60 mg | GSM2140603 | GSM2140603: 60mg arm 1; Danio rerio; RNA Seq | GSM2140603 | 1 | The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2140603 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP074244 | 60mg-arm-1.fastq.gz | fastq | 2471843300.0 | 24718433.0 | GSM2140603 r1 | 0:100 | A:578536744;C:593318438;G:586674975;T:713299111;N:14032 | 100 | 578536744 | 593318438 | 586674975 | 713299111 | 14032 | SRX1738397 | SRS1418769 | SRA422860 | GEO | Chromosome Structure and Development Group, Department of Pathology, University of Otago | 1 | 0.95474 | 0.04276 | 0.75625 | 0.61194 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | New Zealand | 2016-05-02 | Multi-stage | Multi-stage | Oocyte | Reproductive System |