RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.

ABSTRACT: Purpose: Conditional knockout of Zfp36l1 Zfp36l2 early in lymphocyte development leads to a bypass of beta-selection and subsequently T cell acute lymphoblastic leukemia. This RNA seq experiment aimed to determine the molecular pathways affected by loss of Zfp36l1 and Zfp36l2, and to deduce direct targets of these RNA binding proteins. Methods: RNA was isolated from sorted Zfp36l1fl/fl; Zfp36l2fl/fl DN3a (Lineage-negative, CD44-, Kitlow, CD25+, CD98low) and DN3b (Lineage-negative, CD44-, Kitlow, CD25intermediate, CD98+) cells as well as Zfp36l1fl/fl; Zfp36l2fl/fl; CD2cre DN3 (Lineage-negative, CD44-, Kitlow, CD25+) cells with the RNeasy Micro Kit (Qiagen). RNAseq libraries were prepared from 20-200ng RNA using the TruSeq Stranded Total RNA and rRNA Removal Mix – Gold from Illumina. Libraries were sequenced by Hiseq in 100bp single-end reads. The reads were trimmed to remove adapter sequences using Trim Galore then mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly; reads with an identical sequence to more than one genomic locus were not mapped. Quality control analysis was carried out with FastQC. Reads were counted using htseq-count tool and mouse gtf file version 78. Results: Differences in the abundance of transcripts between DCKO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3). Adjusted P values for differential expression were calculated in DESeq2 using a Benjamini-Hochberg correction: genes with an adjusted p-value of less than 5% were considered significant. Differentially expressed mouse transcripts identified using DESeq2 were analyzed for gene set enrichment using Toppfun. Conclusions: We identified an enrichment of mRNAs involved in cell cycle progression within Zfp36l1 Zfp36l2 double conditional knockouts.

ORGANISM(S): Mus musculus

PROVIDER: GSE79174 | GEO | 2016/09/05

SECONDARY ACCESSION(S): PRJNA315110

REPOSITORIES: GEO