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Sample GSM2264216 Query DataSets for GSM2264216
Status Public on Jun 11, 2017
Title Effector Memory- Replicate 2
Sample type SRA
Source name Peripheral whole blood
Organism Homo sapiens
Characteristics cell type: CD4+ Effector Memory (CD45RA lo; CD197 (CCR7) lo)
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-6
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
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
BioSample SAMN05521446
SRA SRX2007331

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

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