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Sample GSM3004526 Query DataSets for GSM3004526
Status Public on Mar 01, 2018
Title KLRG1- Reporter+ OT-I cells (exp1)
Sample type SRA
 
Source name OT-I cell subset purified from spleen
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: wild type
tissue: Spleen
cell type: KLRG1- Reporter+ OT-I cells
treatment: Infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA)
day post-infection: 104
Extracted molecule total RNA
Extraction protocol OT-I cell subsets were isolated from spleen, purified by FACS and RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description S06612
processed data file: Matrix_table.txt
Data processing Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using TopHat2 version 2.0.8.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks version 2.1.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table.txt: Tab-delimited text file includes FPKM values of all six samples.
 
Submission date Feb 14, 2018
Last update date Mar 01, 2018
Contact name Dietmar Herndler-Brandstetter
Organization name Medical University of Vienna
Department Institute of Cancer Research
Street address Borschkegasse 8a
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL18480
Series (2)
GSE110629 Next-generation sequencing of three memory OT-I cell subsets from mice infected with Listeria monocytogenes
GSE110707 KLRG1+ Effector CD8+ T Cells Lose KLRG1, Differentiate Into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity
Relations
BioSample SAMN08536818
SRA SRX3700447

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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