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Sample GSM2264296 Query DataSets for GSM2264296
Status Public on Sep 02, 2016
Title Kat6a-KO, KLRG1-low [3a]
Sample type SRA
 
Source name CD8+ T cells
Organism Mus musculus
Characteristics background strain: C57BL/6
genotype: Kat6a knock-out
infection: Infected, KLRG1-low
Treatment protocol P14 transgenic CD8+ T cells were isolated directly ex vivo from the spleen of naïve mice or those infected for eight days with LCMV-WE.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 3a
Data processing FASTQ files were output using standard Illumina protocols and Illumina CASAVA sofware version 1.8.2.
Reads were aligned to the mouse genome with subread 1.4.4.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in RefSeq annotation.
Read counts from technical replicates of the same sample were summed.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.
 
Submission date Aug 08, 2016
Last update date May 15, 2019
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL13112
Series (1)
GSE85302 KAT6A determines CD8+ T cell diversity via regulation of co-receptors
Relations
BioSample SAMN05521529
SRA SRX2007434

Supplementary file Size Download File type/resource
GSM2264296_3a_counts.tsv.gz 169.6 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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