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Sample GSM3736898 Query DataSets for GSM3736898
Status Public on Aug 23, 2020
Title 39_319_CD4CD8_GFPpos
Sample type SRA
Source name CD4 positive T Cells
Organism Homo sapiens
Characteristics subjectid: S319
Sex: male
culture: CD4CD8
egfp: GFPpos
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
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
BioSample SAMN11515489
SRA SRX5758353

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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