|
Status |
Public on Apr 15, 2016 |
Title |
LH097_N |
Sample type |
SRA |
|
|
Source name |
Donor LH097 Naïve T cells
|
Organism |
Homo sapiens |
Characteristics |
donor id: LH097 cell type: naive T cells
|
Extracted molecule |
polyA RNA |
Extraction protocol |
T cell subsets were sorted by fluorescence activated cell sorting (FACS) and total RNA was extracted using Trizol and isopropanol precipitation. Poly(A)+ mRNA was then isolated from each total RNA sample using streptavidin-coated superparamagnetic beads (Dynabeads, Life Technologies) coated in biotinylated LNA-oligo(dT) (Exiqon). Purified poly(A)+ mRNA from each sample was reverse transcribed and Illumina sequencing libraries were enriched usign the SMARTer Stranded RNA-Seq kit (Clontech). The resulting libraries were sequenced on an Illumina NextSeq 500 with single-end 75-base reads.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Reads were mapped to the Ensembl GRCh37 human genome and transcriptome annotation (obtained from Illumina iGenomes) using Tophat 2 and uniquely mapped reads associated with each gene were counted using HTSeq. Genome_build: mm10 Supplementary_files_format_and_content: tab-delimited table of raw counts of uniquely mapped reads for each gene
|
|
|
Submission date |
Apr 14, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Peter A Sims |
E-mail(s) |
pas2182@columbia.edu
|
Organization name |
Columbia University
|
Street address |
3960 Broadway, Lasker 203AC
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10032 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE80306 |
Aging-related virtually naïve memory T (TVNM) cells: a new stage in T cell response to persistent infections in humans |
|
Relations |
BioSample |
SAMN04857193 |
SRA |
SRX1705752 |