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Sample GSM1483122 Query DataSets for GSM1483122
Status Public on Sep 11, 2014
Title gBT-TRM+PBS_rep2_sample2
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 149_8
Sample 36
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
E-mail(s) s.ariotti@nki.nl
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
Relations
BioSample SAMN03000769
SRA SRX684429

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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