|
| Status |
Public on Apr 23, 2015 |
| Title |
TH17 Primary_2695 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear
polarizing conditions: TH17
rna fraction: polyA+ RNA
|
| Treatment protocol |
Cells were treated with cytokine and antibody cocktails detailed above to generate TH1, TH2, and TH17 in vitro cultures from healthy human donors.
|
| Growth protocol |
Human PBMC were isolated from healthy volunteers and stimulated with soluble mouse anti-human CD28 (1 mg/ml; 555725; BD Biosciences) and plate-bound anti-CD3 (10 mg/ml; OKT3 clone American Type Culture Collection), 1 x 10^6 cells/ml, under TH1: IL-12 (10 ng/ml), TH2: IL-4 (10 ng/ml), or TH17: IL-1b (20 ng/ml), IL-6 (50 ng/ml), IL-23 (20 ng/ml), IL-21 (100 ng/mL), TGF-b1 (5 ng/ml) and mouse anti-human IFN-g (10 mg/ml; 554698; BD Biosciences), polarizing conditions. TH1 and TH2 cultures were harvested after 5 days to obtain RNA from primary cultures. TH17 cultures were harvested after 7 days to obtain RNA from primary cultures. After 5 days (TH1 and TH2) or 7 days (TH17), cultures were restimulated with plate-bound anti-CD3 and harvested 2 days later to obtain RNA from effector cultures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRI Reagent (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.
"2695" libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol. "2960" libraries were constructed using the Illumina TruSeq Stranded Total RNA kit (Catalog No. RS-122-2201) following the manufacturer's supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2695-TA-3
|
| 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: Read Count Table
|
| |
|
| Submission date |
Feb 24, 2015 |
| 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 |
GPL16791 |
| Series (1) |
| GSE66261 |
Expression and functions of long noncoding RNAs during human T helper cell differentiation |
|
| Relations |
| BioSample |
SAMN03372112 |
| SRA |
SRX889711 |
