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Series GSE79174 Query DataSets for GSE79174
Status Public on Sep 05, 2016
Title RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design 4 biological replicates of control DN3a, control DN3b and DCKO DN3-like cells were analyzed
 
Contributor(s) Vogel KU, Ahlfors H, Turner M
Citation(s) 27566829
Submission date Mar 14, 2016
Last update date May 15, 2019
Contact name Martin Turner
E-mail(s) martin.turner@babraham.ac.uk
Organization name Babraham Institute
Department Lymphocyte Signalling and Development
Lab Dr. Martin Turner
Street address Babraham Hall
City Cambridge
ZIP/Postal code CB22 3AT
Country United Kingdom
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM2087300 Control DN3a_1
GSM2087301 Control DN3b_1
GSM2087302 Control DN3a_2
This SubSeries is part of SuperSeries:
GSE79179 Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice
Relations
BioProject PRJNA315110
SRA SRP071732

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE79174_DESeq2_out_KO_DN3_vs_WT_DN3a.txt.gz 840.0 Kb (ftp)(http) TXT
GSE79174_DESeq2_out_KO_DN3_vs_WT_DN3b.txt.gz 825.6 Kb (ftp)(http) TXT
GSE79174_DESeq2_out_WT_DN3b_vs_WT_DN3a.txt.gz 843.7 Kb (ftp)(http) TXT
GSE79174_Vogel_normData.txt.gz 1.2 Mb (ftp)(http) TXT
GSE79174_Vogel_rawData.txt.gz 522.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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