|
| Status |
Public on Jun 23, 2020 |
| Title |
Doc5_neg_rep1 (ATAC-seq) |
| Sample type |
SRA |
| |
|
| Source name |
ID3neg_Docile_day5
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Male
tissue: spleen
cell type: ID3GFP- P14 T cells
infection: LCMV Docile
time: day5
|
| Growth protocol |
P14 T cells were transferred into naïve mice and challenged with LCMV Docile or Armstrong; cells were isolated based on ID3GFP and TIM3 expression
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using cell lysis buffer as described previously (Buenrostro, et al 2013)
Libraries were generated following the protocol as described previously (Buenrostro, et al 2013)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Doc5n1
|
| Data processing |
The paired-end libraries were mapped to the GRCm38/mm10 reference genome by using Subread-1.6.2. Only uniquely mapped read-pairs were allowed in mapping. Peaks were then called from the mapping results by using Homer (v4.9) at an FDR cutoff of 1E-5.
The peaks from all the samples were merged by taking the union of the peaks; the merged peaks were then assigned to the nearest genes in the NCBI RefSeq gene annotation for mm10 (build 38.1). The mapped read-pairs were assigned to the merged peak regions by using featureCounts.
Merged peaks were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.7 in at least 2 libraries. Counts were converted to log2 CPM values, library normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each merged peak, and empirical Bayes moderated t-statistics were used to assess differences of accessibility of the chromatin. Merged peaks were called differential if they achieved a false discovery rate of 0.2 or less, and have a fold change greater than 2 between the two compared cell types.
Genome_build: mm10
Supplementary_files_format_and_content: Supp_Raw_Counts.txt
tab-delimited files consisting of log2 CPM (counts per million mapped reads) values of peaks and their corresponding genes
|
| |
|
| Submission date |
Dec 24, 2019 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Wei Shi |
| E-mail(s) |
wei.shi@onjcri.org.au
|
| Organization name |
Olivia Newton-John Cancer Research Institute
|
| Lab |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
Victoria |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE142575 |
Early precursor T cells establish and propagate T cell exhaustion in chronic infection [ATAC-seq] |
| GSE142687 |
Early precursor T cells establish and propagate T cell exhaustion in chronic infection |
|
| Relations |
| BioSample |
SAMN13676403 |
| SRA |
SRX7438451 |
