|
Status |
Public on Sep 11, 2014 |
Title |
OTI-TRM+OVApep_sex mismatched_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 2068_6 Sample 20
|
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 |
SAMN03000753 |
SRA |
SRX684413 |