|
| Status |
Public on Jan 08, 2018 |
| Title |
WT2_CD25+ |
| Sample type |
SRA |
| |
|
| Source name |
WT_CD25+_CD4+ YFP+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Foxp3-IRES-YFP-Cre
cell type: CD4+ YFP+ T cells
|
| Treatment protocol |
No treament.
|
| Growth protocol |
T cells were cultured in DMEM medium supplemented with 10%FBS, 1x non-essential amino acids, 10 mM HEPES, pH7.4, 50 µM β-mercaptoethanol at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
T cells were isolated from the spleen and lymph nodes, then sorted for CD4+ YFP+ CD25+ or CD4+ YFP+ CD25- and finally lysed in TRIzol.
RNA libraries from the sorted CD25+ or CD25- Treg (CD4+ YFP+) cells were prepared according to the Encore Complete RNA-Seq DR Multiplex Systems (NuGEN Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
processed data file: tregs_rnaseq_counts.csv
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse transcriptome based on RefSeq (RNA-seq) using segemehl v0.1.7-411 with parameters --accuracy 90.
Transcript counts were calculated based on uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample (RNA-seq).
|
| |
|
| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joao C Guimaraes |
| E-mail(s) |
joaoguima@gmail.com
|
| Organization name |
University of Basel
|
| Department |
Biozentrum
|
| Street address |
Klingelbergstrasse 50 / 70
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE86110 |
Roquin suppresses PI3K-mTOR signaling to control T cell differentiation and Treg effector function |
|
| Relations |
| BioSample |
SAMN07357668 |
| SRA |
SRX3009091 |
