|
| Status |
Public on Feb 08, 2018 |
| Title |
RNA_HDM_cMaf_flfl_CD4Cre_3 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells (Th2 HDM allergy model)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: c-Maf flfl CD4Cre
background strain: C57BL/6
tissue: Lung
cell type: CD4+ T cell
time point: day 25 of HDM induced allergy
|
| Treatment protocol |
c-Maf flfl CD4Cre mice were sensitized with 10 mg HDM (Greer) or PBS and 2mg Imject Alum (Thermo Scientific) by intraperitoneal injections on days 0 and 14, and challenged intratracheally with 10 mg HDM or PBS on days 21 and 24.
|
| Growth protocol |
On day 25, CD4+ T cells were enriched from perfused lungs (pooled) following a Percoll gradient separation by positive selection using anti-CD4 microbeads (Miltenyi Biotech). After staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD8 FITC, anti-CD4-eFluor450 and anti-CD44-PE (eBioscience), CD3+CD8-CD4+CD44+ 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 |
SAMN07967659 |
| SRA |
SRX3355832 |
