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Sample GSM1618314 Query DataSets for GSM1618314
Status Public on Apr 23, 2015
Title TH1 Effector_2695
Sample type SRA
 
Source name PBMC
Organism Homo sapiens
Characteristics cell type: peripheral blood mononuclear
polarizing conditions: TH1
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-4
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 SAMN03372113
SRA SRX889712

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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