|
| Status |
Public on May 29, 2018 |
| Title |
CD8_D0_3 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
splenic CD8T cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
replicate: 3
ly49expression: NA
condition: MCMVD0
cell type: splenic CD8T cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lymphocytes were harvested as described in manuscript.
Fresh cells were prepared as previously described (Buenrostro et al., 2013). Briefly, cells were washed in cold PBS and lysed. Transposition occurred at 42°C for 45 minutes. DNA was purified using the MinElute PCR purification kit (Qiagen) and amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina). An average of 51 million paired reads were generated per sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
BCL files were converted to fastq using bcl2fastq (v2.16-2.19).
ATAC-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on Tn5-shifted, concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 from peak regions among all samples within each experiment.
|
| |
|
| Submission date |
Dec 13, 2017 |
| Last update date |
Aug 06, 2018 |
| Contact name |
Colleen Lau |
| Organization name |
Cornell University
|
| Department |
Microbiology & Immunology
|
| Street address |
930 Campus Road
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106139 |
Regulation of natural killer cells during MCMV infection |
| GSE108051 |
Epigenetic control of innate and adaptive immune memory [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN08173893 |
| SRA |
SRX3469043 |
