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Sample GSM1483099 Query DataSets for GSM1483099
Status Public on Sep 11, 2014
Title OTI-TRM+gBpep_rep1_sample1
Sample type SRA
Source name full-thickness skin
Organism Mus musculus
Characteristics strain: C57Bl6/j
tissue: skin
genotype: wild type
Treatment protocol Mice were tattoo-vaccinated in the hind legs with 2µg DNA TTFC carrier protein plus the indicated peptide in order to induce a population of skin-resident memory T cells. Mice were used for experiments at least three weeks after vaccination (memory phase).
Extracted molecule total RNA
Extraction protocol Skin harboring tissue resident memory T cells was injected with virus or peptide. 9 hours later, the mouse was sacrificed, full-thickness skin collected and snap-frozen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description datarun 2026_8
Sample 13
Data processing All samples were aligned using Tophat and readcounts were calculated with Htseq-count
Sample 1-6 were aligned using Tophat version 1.3.1 based on ensembl version 64 with parameters --library-type fr-unstranded -G
Sample 7-10,29-36 were aligned using Tophat version 1.4.0 based on ensembl version 66 with parameters --library-type fr-unstranded -G --transcriptome-index
Sample 11-28,37-45 were aligned using Tophat version 2.0.6 based on ensembl version 66 with parameters --bowtie 1 --library-type fr-unstranded -no-coverage-search -M -transcriptome-index
Genome_build: mm9
Supplementary_files_format_and_content: The file genecounts_all.txt contains the absolute readcounts as a result from Htseq-count. Genes that have 0 readcounts across all samples were removed.
Submission date Aug 21, 2014
Last update date May 15, 2019
Contact name silvia ariotti
Organization name NKI
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
Platform ID GPL13112
Series (1)
GSE60599 Genome wide transcriptome analysis of skin harboring tissue-resident memory CD8+ T cells
BioSample SAMN03000746
SRA SRX684406

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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