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RNA-seq to identify differentially expressed mRNAs after cKO of Ybx1 in DRG [RNA-seq]

ABSTRACT: RNA-seq to identify differentially expressed mRNAs after cKO of Ybx1 in DRG [RNA-seq]

PROVIDER: PRJNA1074801 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27922628_1.fastq.gz	Fastqsanger.gz
	SRR27922628_2.fastq.gz	Fastqsanger.gz
	SRR27922629_1.fastq.gz	Fastqsanger.gz
	SRR27922629_2.fastq.gz	Fastqsanger.gz
	SRR27922630_1.fastq.gz	Fastqsanger.gz

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RNA-seq to identify differentially expressed mRNAs after cKO of Ybx1 in DRG [RNA-seq]

Project description:To identify the target mRNAs of Ybx1 in mouse DRG, we first performed RNAseq to screen differentially expressed mRNAs after knockout of Ybx1. We generated Wnt1-cre+/-;Ybx1fl/fl cKO mice to specifically knockout Ybx1 in DRG. Then we collected E13.5 DRG from cKO mice and litermate Ybx1fl/fl control mice. After RNA extraction and library construction, RNA sequcencing was performed. Finally, we identified 1638 differentially expressed mRNAs. This study provides a gene list which shows mRNA that can be regulated by Ybx1 in mouse DRG.

2024-11-15 | GSE255394 | GEO

Anti-Ybx1 RIP-seq to identify target mRNAs of Ybx1 in E13.5 DRG [RIP-seq]

Project description:In order to identify the target mRNAs of the m5C reader protein Ybx1, we carried out anti-Ybx1 RNA Immunoprecipitation(RIP) followed by RNA-sequencing to find out mRNAs that can directly bind by Ybx1. Using EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from E13.5 wildtype mouse DRGs was pulled down by rabbit monoclonal anti-Ybx1 (abcam) and sequenced on IIIumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm39) using BWA mem (v 0.7.12). After peak calling using MACS2 (version 2.1.0) software, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed. Fold enrichment greater than 2 was considered to be enriched. Finally, 2 biological repilicates of anti-Ybx1 RIP-seq identified 2487 transcripts. This study provides a gene list which shows mRNA binding with Ybx1 in mouse DRGs.

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Anti-Ybx1 RIP-seq to identify target mRNAs of Ybx1 in E13.5 DRG [RIP-seq]

Project description:Anti-Ybx1 RIP-seq to identify target mRNAs of Ybx1 in E13.5 DRG [RIP-seq]

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Project description:In order to identify YBX1 binding sites on tRNA fragments, we performed small-RNA HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Chi SW, et al. 2009, Nature 460:479)

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Project description:In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Licatalosi D, et al. 2008, Nature 456:464-U22)

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