|
| Status |
Public on May 18, 2016 |
| Title |
Control 5 |
| Sample type |
SRA |
| |
|
| Source name |
OT-I T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Lymph node
|
| Treatment protocol |
5 mM acetate was added during the last 3 days of culture
|
| Growth protocol |
OVA-specific OT-I memory T cells were activated with 10^–9 M OVA peptide in the presence of splenocytes for 3 d, followed by 3-4 d culture in IL-15 (10 ng/mL) in absence of OVA peptide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA input material was used to make barcoded and ready to sequence libraries using the Illumina TruSeq Stranded mRNA Sample Preparation Kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The prepared libraries were sequenced on the Illumina NextSeq 500 using a v2 kit with 75 cycles and high output.
The resulting reads were mapped to the mm10 reference genome using the STAR software version 2.4.0h (GitHub, Inc.).
Resulting mapping files in bam format were analyzed using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) from the HTSeq framework (version 0.6.0) for read count numbers to specific genomic features (whole genes).
Finally, the raw count files were inputted to the statistical analysis software DESeq2 (version 1.6.3) from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: mapped raw read counts
|
| |
|
| Submission date |
Mar 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Hess |
| E-mail(s) |
chess@uhbs.ch
|
| Organization name |
University Basel
|
| Department |
Department of Biomedicine
|
| Lab |
Immunobiology
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE79600 |
Memory CD8+ T cells require stress-levels of acetate for optimal function |
|
| Relations |
| BioSample |
SAMN04579673 |
| SRA |
SRX1661567 |
