|
| Status |
Public on May 31, 2018 |
| Title |
CD8+ T cells 2 |
| Sample type |
SRA |
| |
|
| Source name |
Naïve CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57B/6 male
tissue: Spleen
cell type: T lymphocytes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ HiC was performed as described by Rao et al (Cell 2014; PMID: 25497547).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.
|
| |
|
| Submission date |
Oct 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE105918 |
In situ Hi-C profiles of mouse CD4+ T cells, CD8+ T cells and B cells |
|
| Relations |
| BioSample |
SAMN07823520 |
| SRA |
SRX3314671 |
