|
| Status |
Public on Feb 08, 2018 |
| Title |
RNA_EAE_cMaf_flfl_1 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells (Th17 EAE model)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: c-Maf flfl
background strain: C57BL/6
tissue: CNS (brain and spinal cord)
cell type: CD4+ T cell
time point: day 14-16 post EAE induction
|
| Treatment protocol |
c-Maf flfl mice were immunised subcutaneously with 250 ug MOG35-55 peptide (Cambridge Research Biochemicals) emulsified in complete Freund’s adjuvant containing 250 ug heat-killed M. tuberculosis H37RA (Difco Laboratories) on day 0. On days 0 and 2 post immunisation, mice received 200ng pertussis toxin (Calbiochem) intraperitoneally.
|
| Growth protocol |
On day 14-16, CD4+ T cells were isolated from brains and spinal cords (pooled) following a Percoll gradient separation and staining in PBS with 5% FCS for 20 min at 4C with anti-CD45.2-PE, anti-CD11b-FITC, anti-CD3-APC and anti-CD4-eFluor450. CD8-CD45.2+CD3+CD4+ T cells were sorted on MoFloTM XDP (Beckman Coulter) cytometer
|
| 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 |
SAMN07967675 |
| SRA |
SRX3355821 |
