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Sample GSM850875 Query DataSets for GSM850875
Status Public on Aug 08, 2012
Title RNA-seq of mock (untreated) CD4+ T cells
Sample type SRA
 
Source name CD4+ T cells_untreated
Organism Mus musculus
Characteristics strain: C57BL/6JJcl
gender: male
cell type: CD4+ T cells
treatment: Mock treated as below, but omitting the antibodies
Treatment protocol Cells were treated with plate-immoblised anti-CD3e (2 ug/ml) and anti-CD28 (2 ug/ml) for 4 hours or were mock treated identically but omitting the antibody. Total RNA was harvested using TRIzol according to the manufacturers protocol
Growth protocol CD4+ T cells were purified from 4 pooled mice spleens using the BD IMag CD4+ T cell enrichment kit -DM, according to the manufacturers instructions.
Extracted molecule total RNA
Extraction protocol Library and Sequencing were performed at BGI, China. Library Constuction and Sequencing were performed using standard Illumnina kits and protocols. Insert sizes were 199.014 bp for anti-CD3/CD28 treated CD4+ T cells and 211.79 bp for Mock treated CD4+ T cells
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNA-seq of mock (untreated) CD4+ T cells
Data processing TCD4_mock-junctions.bed; genome build: mm9
Alignment: Sequence reads were aligned to the mm9 mouse genome assembly using the TopHat and Cufflinks combination
Splice Junctions: A bed file containing the splice junctions as determined by the TopHat and Cufflinks combination
 
Submission date Dec 19, 2011
Last update date May 15, 2019
Contact name Andrew P Hutchins
E-mail(s) andrewh@sustech.edu.cn
Organization name Southern University of Science and Technology
Department Bioinformatics
Lab Bioinformatics and Genomics
Street address 1088 Xueyuan Rd
City Shenzhen
ZIP/Postal code 518055
Country China
 
Platform ID GPL13112
Series (1)
GSE34550 Systematic RNA-seq analysis of the early events of CD4+ T cell activation
Relations
SRA SRX112210
BioSample SAMN00767526

Supplementary file Size Download File type/resource
GSM850875_TCD4_mock-junctions.bed.gz 1.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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