|
| Status |
Public on Feb 08, 2018 |
| Title |
RNA_MAL_cMaf_flfl_CD4Cre_3 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells (Th1 malaria model)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: c-Maf flfl CD4Cre
background strain: C57BL/6
tissue: Spleen
cell type: CD4+ T cell
time point: day 7 post Plasmodim chabaudi chabaudi AS infection
|
| Treatment protocol |
c-Maf flfl CD4Cre mice were infected with 105 Plasmodim chabaudi chabaudi AS infected red blood cells on day 0.
|
| Growth protocol |
On day 7 post infection, CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD4-eFluor450, anti-CD8 FITC (eBioscience) and anti-Ter119-APCCy7 (BD). Live (propidium iodide negative) Ter119-CD3+CD8-CD4+ T cells were sorted using on a MoFloTM XDP (Beckman Coulter) or BD Fusion cytometers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was carried out using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
Libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignment of reads to the mouse transcriptome (mm10) and absolute quantification of the genes was performed in Strand NGS (version 2.0) with default parameters (95% identity, max 5% gaps, 1 read only if duplicated, ignoring reads with more than 5 matches) guided by Ensembl (2014.04.01) annotations.
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided for RNA-seq data normalised to RPKMs
|
| |
|
| Submission date |
Nov 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Leona Gabrysova |
| E-mail(s) |
Leona.Gabrysova@crick.ac.uk
|
| Phone |
+442037961441
|
| Organization name |
The Crick Institute
|
| Lab |
Immunoregulation and Infection Lab
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106462 |
The transcription factor c-Maf is a positive regulator of IL-10 with context-specific roles in CD4+ T cell effector function and in vivo consequences [RNA-seq in vivo] |
| GSE106464 |
The transcription factor c-Maf is a positive regulator of IL-10 with context-specific roles in CD4+ T cell effector function and in vivo consequences |
|
| Relations |
| BioSample |
SAMN07967667 |
| SRA |
SRX3355838 |
