|
| Status |
Public on Jun 11, 2017 |
| Title |
Central Memory- Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+ Central Memory (CD45RA lo; CD197 (CCR7) hi)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral whole blood was collected into BD Vacutainer tubes. Peripheral blood mononuclear cells were isolated using SepMate-50 tubes according to the manufacturer's supplied protocol (Stem Cell Technologies). CD4+ T cells were enriched using the EasySep Human CD4+ T cell enrichment kit and subsequently labeled with the BD Biosciences Naive/Memory T-cell panel (#561438) prior to fluorescence activated cell sorting.
Total RNA isolated using TriReagent (Molecular Research Center) and purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
The 3026 project library was constructed using the Illumina TruSeq Stranded Total RNA Library Prep kit (Cat. No. RS-122-2201) following the manufacturer's supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
3026-TA-8
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file, read count table
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles F Spurlock III |
| E-mail(s) |
chase.spurlock@vanderbilt.edu
|
| Phone |
6153432363
|
| Organization name |
Vanderbilt University School of Medicine
|
| Department |
Medicine
|
| Lab |
T3113
|
| Street address |
1161 21st Avenue South
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE85294 |
Profiles of Long Noncoding RNAs in Human Naive and Memory T Cells |
|
| Relations |
| BioSample |
SAMN05521444 |
| SRA |
SRX2007333 |
