|
Status |
Public on Jun 23, 2020 |
Title |
Doc5_pos_rep3 (ATAC-seq) |
Sample type |
SRA |
|
|
Source name |
ID3pos_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)
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|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Doc5p3
|
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
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|
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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 |
SAMN13676399 |
SRA |
SRX7438454 |