|
| Status |
Public on Mar 01, 2018 |
| Title |
Day 8 KLRG1- Reporter+ OT-I cells (exp2) |
| Sample type |
SRA |
| |
|
| Source name |
OT-I cell subset purified from spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wild type
tissue: Spleen
cell type: KLRG1- Reporter+ OT-I cells
treatment: Infection with ovalbumin-expressing Listeria monocytogenes
days post-infection: 8
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
OT-I cell subsets were isolated from spleen, purified by FACS and DNA was extracted from 50,000 OT-I cell subsets using cold lysis buffer (as described by Buenrostro et al. 2015).
Nuclei pellets were resuspended in the transposition reaction mix (Nextera Kit) and incubated at 37°C for 30 min. Qiagen MinElute PCR Purification Kit was used to purify DNA. To amplify transposed DNA fragments, PCR with barcoded PCR primers (Buenrostro et al., 2013) and NEBNext High-Fidelity 2x PCR Master Mix was performed. To reduce GC and size bias in PCR, the appropriate number of PCR cycles was determined using qPCR. The amplified library was purified using a Qiagen MinElute PCR Purification Kit.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing reads were first processed with cutadapt-1.8.3 (Martin, 2011) to trim adapters.
Bowtie-2 (Langmead and Salzberg, 2012) was used then to align the trimmed reads to the mouse genome mm10 with default parameters. Duplicated reads were marked and removed from the analysis with Picard MarkDuplicate tool (http://broadinstitute.github.io/picard).
BEDTools (Quinlan and Hall, 2010) was used to turn the alignment file to a bed file, which was the input of MACS2 (Zhang et al., 2008) to call peaks and produce BedGraph files.
Visualizations of coverage on regions of interest were produced with IGV (Robinson et al., 2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_treat_pileup.bedgraph: bedGraph files include peak calls.
|
| |
|
| Submission date |
Feb 20, 2018 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Dietmar Herndler-Brandstetter |
| Organization name |
Medical University of Vienna
|
| Department |
Institute of Cancer Research
|
| Street address |
Borschkegasse 8a
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE110707 |
KLRG1+ Effector CD8+ T Cells Lose KLRG1, Differentiate Into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity |
| GSE110876 |
ATAC-seq of naive and three effector OT-I cell subsets from mice infected with Listeria monocytogenes |
|
| Relations |
| BioSample |
SAMN08568318 |
| SRA |
SRX3726854 |
