run_metadata: 77314
This data as json
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| 77314 | SRR25453766 | SRX21186674 | SRS18446695 | 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 10 tgher4:RFP tgmcm5:gfp | GSM7668456 | source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r10|geo loc name:missing|collection date:missing | Experiment 10 tgher4:RFP tgmcm5:gfp | 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 tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r10 | GSM7668456 | GSM7668456: Experiment 10 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq | GSM7668456 r1 | GSM7668456 | 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 | 10RG.fastq.gz | fastq | 1331151616.0 | 20799244.0 | GSM7668456 r1 | 0:64 | A:310326669;C:355505465;G:405609592;T:259699955;N:9935 | 64 | 310326669 | 355505465 | 405609592 | 259699955 | 9935 | SRX21186674 | SRS18446695 | SRA1682601 | Institut Pasteur | Institut Pasteur | 1 | 0.8952 | 0.2601 | 0.7769 | 0.6903 | 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 |