|
| Status |
Public on Feb 08, 2018 |
| Title |
ATAC_MAL_cMaf_flfl_2 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells (Th1 malaria model)
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL6
genotype: c-Maf flfl
tissue: Spleen
cell type: CD4+ T cell
time point: day 7 post Plasmodim chabaudi chabaudi AS infection
|
| Treatment protocol |
c-Maf flfl 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-CD4-eFluor450, anti-CD3-APC (eBioscience) and anti-Ter119-APCCy7 (BD). Live (propidium iodide negative) Ter119-CD3+CD4+ T cells were sorted using on a MoFloTM XDP (Beckman Coulter) or BD Fusion cytometers.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells sorting was followed by a transposition reaction and purification, prepared as in Buenrostro et al. Curr Protoc Mol Biol. 2015 with the transposition reaction carried out for 1h and 30 minutes at 37 °C and subsequent PCR amplification for 12 cycles
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 with BWA-MEM
Duplicates were removed using Picard
alignment QC, discarded alignments with a mapQ below 30 using SAMtools 1.3.1
Discarded alignemnts done to mitochondrial DNA, shifted Reads to represent the Tn5 insertion, and remove fragments spanning nucleosomes (size >99 bp) using awk and BEDTools 2.4.2. Fragments spanning nucleosomes were not removed for the one untreated sample
MACS2 2.1.1 (parameters --keep-dup all, --nomodel, --shift -100, --extsize 200) was used to call peaks (q-value < 0.01)
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 ATAC-seq data normalised to RPKMs (fragments spanning nucleosomes excluded), for peaks called bed files are provided
|
| |
|
| 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) |
| GSE106461 |
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 [ATAC-seq] |
| 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 |
SAMN07967684 |
| SRA |
SRX3355844 |
