run_metadata: 77303
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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| 77303 | SRR25453755 | SRX21186685 | SRS18446706 | SRP452071 | PRJNA999746 | Transcriptomic differences between deeply quiescent and activated adult NSCs | GSE239594 | Transcriptome Analysis | To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq | parent bioproject:PRJNA999741 | pubmed:38518783 | Experiment 13 tgher4:RFP low | GSM7668467 | source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r13|geo loc name:missing|collection date:missing | Experiment 13 tgher4:RFP low | Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts | brain/telencephali | PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories | tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r13 | GSM7668467 | GSM7668467: Experiment 13 tgher4:RFP low; Danio rerio; RNA Seq | GSM7668467 r1 | GSM7668467 | 1 | PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP452071 | 13RL.fastq.gz | fastq | 2089168000.0 | 32643250.0 | GSM7668467 r1 | 0:64 | A:491435480;C:556848569;G:626704317;T:414165769;N:13865 | 64 | 491435480 | 556848569 | 626704317 | 414165769 | 13865 | SRX21186685 | SRS18446706 | SRA1683289 | Institut Pasteur | Institut Pasteur | 1 | 0.8119 | 0.23552 | 0.78575 | 0.66137 | 64 | B | usable mapping rate | illumina | hiseq_era | full_length | cdna_unspecified | smarter | bulk | bulk | bulk | France | 2023-07-28 | Adult | Adult | Brain | Nervous System |