|
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 |