run_metadata: 77312
This data as json
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| 77312 | SRR25453760 | SRX21186680 | SRS18446701 | 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 12 tgher4:RFP tgmcm5:gfp | GSM7668462 | source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r12|geo loc name:missing|collection date:missing | Experiment 12 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:r12 | GSM7668462 | GSM7668462: Experiment 12 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq | GSM7668462 r1 | GSM7668462 | 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 | 12RG.fastq.gz | fastq | 1740870592.0 | 27201103.0 | GSM7668462 r1 | 0:64 | A:415787017;C:459034090;G:503793126;T:362245237;N:11122 | 64 | 415787017 | 459034090 | 503793126 | 362245237 | 11122 | SRX21186680 | SRS18446701 | SRA1682601 | Institut Pasteur | Institut Pasteur | 1 | 0.89438 | 0.32229 | 0.75237 | 0.62254 | 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 |