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Sample GSM871914 Query DataSets for GSM871914
Status Public on Feb 09, 2012
Title TCRa-1
Sample type SRA
 
Source name CD8+ thymocytes
Organism Mus musculus
Characteristics strain: C57Bl/6
cell type: CD8+ thymocytes
Growth protocol Seven-week-old C57Bl/6 mice were purchased from Harlan laboratory
Extracted molecule total RNA
Extraction protocol 1 mg of total RNA from CD8+ T cell was used for TCR amplification, using specific primer in the constant region fused with the T7 promoter. The in vitro transcription was performed according to the instructions of the MessageAmp II aRNA Amplification Kit (Ambion, Rotkreuz, Switzerland).
Illumina sequencing: A specific ssDNA adapter (adenyl-AGATCGGAAGAGCGGTTCAGddC) was ligated to the 3' end of the RNA fragments using truncated T4 RNA ligase. The first strand cDNA was then synthesized using a primer (CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT) complementary to the ssDNA adapter. The library was prepared by adding the Illumina adapters sequences by PCR amplification using a primer specific to the 5' constant region (AATGATACGGCGACCACCGAGATCTACACAGCAGGTTCTGGGTTCTG) and the standard Illumina PCR primer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description TCRa mRNA
Data processing Each processed data file contains three tab delimited files for each TRAJ gene segment identified by sequencing:
TRAJ*.gnt : in-frame TCRalpha chains containing a uniquely identified TRAV segment
TRAJ*.red : in-frame and out-of-frame TCRalpha chains containing a TRAV segment that could not be uniquely identified
TRAJ*.bnt : out-of-frame TCRalpha chains containing a uniquely identified TRAV segment
 
Submission date Feb 08, 2012
Last update date May 15, 2019
Contact name Brian James Stevenson
E-mail(s) brian.stevenson@unil.ch
Organization name Swiss Institute of Bioinformatics
Street address Genopode, UNIL-Sorge
City Lausanne
ZIP/Postal code CH-1015
Country Switzerland
 
Platform ID GPL13112
Series (1)
GSE35626 HIGHLY DIVERSE TCRalpha CHAIN REPERTOIRE OF PRE-IMMUNE CD8+ T CELLS REVEALS NEW INSIGHTS IN GENE RECOMBINATION
Relations
SRA SRX119105
BioSample SAMN00783788

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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