|
| Status |
Public on Apr 15, 2016 |
| Title |
LH083_CM |
| Sample type |
SRA |
| |
|
| Source name |
Donor LH083 Central Memory T cells
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: LH083
cell type: Central memory 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 |
SAMN04857201 |
| SRA |
SRX1705760 |
