|
| Status |
Public on Sep 11, 2014 |
| Title |
OTI-TRM+OVApep_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 MiSeq |
| |
|
| Description |
datarun 2760_2 MiSeq!
Sample 16
|
| 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 |
GPL16417 |
| Series (1) |
| GSE60599 |
Genome wide transcriptome analysis of skin harboring tissue-resident memory CD8+ T cells |
|
| Relations |
| BioSample |
SAMN03000749 |
| SRA |
SRX684409 |
