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Sample GSM3736871 Query DataSets for GSM3736871
Status Public on Aug 23, 2020
Title 6_914_CD4_GFPneg
Sample type SRA
 
Source name CD4 positive T Cells
Organism Homo sapiens
Characteristics subjectid: S914
Sex: female
culture: CD4
egfp: GFPneg
Extracted molecule total RNA
Extraction protocol Sorted populations were stored in 350l of RLT buffer with 1% of 2-Mercaptoethanol (BME) at -80°C, purified using Qiagen RNeasy Micro columns, and RNA quality was assessed using an Agilent Bioanalyzer.
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Illumina NexteraXT DNA Library Preparation kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description 616_Michelle_CD4-CD4CD8_DESeq2_NormCounts.txt
Data processing Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
 
Submission date Apr 26, 2019
Last update date Aug 23, 2020
Contact name Gregory K Tharp
E-mail(s) gktharp@emory.edu
Phone 404-727-7797
Organization name Yerkes National Primate Research Center
Department Developmental and Cognitive Neuroscience
Lab Genomics Core
Street address 954 Gatewood Dr
City Atlanta
State/province GA
ZIP/Postal code 30329-4208
Country USA
 
Platform ID GPL21290
Series (1)
GSE130368 Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription
Relations
BioSample SAMN11515484
SRA SRX5758326

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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