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Sample GSM2087301 Query DataSets for GSM2087301
Status Public on Sep 05, 2016
Title Control DN3b_1
Sample type SRA
 
Source name thymus
Organism Mus musculus
Characteristics cell type: pre-T cell, lymphocyte
genotype: Zfp36l1fl/fl, Zfp36l2fl/fl
strain: C57BL/6
Extracted molecule total RNA
Extraction protocol Cells FACS sorted from thymus as described in summary above (methods). RNA was extracted using RNeasy Micro Kit
20-200 ng of RNA used to make libraries using TruSeq Stranded Total RNA and rRNA Removal Mix – Gold from Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description KV2
Data processing Libraries were sequenced by Hiseq 2000 in 100bp single-end reads
Basecalling was done using Illumina default pipeline
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between DCKO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample, and output from DESeq2 analysis
 
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
 
Platform ID GPL13112
Series (2)
GSE79174 RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.
GSE79179 Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice
Relations
BioSample SAMN04549411
SRA SRX1630329

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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