|
| Status |
Public on Mar 27, 2024 |
| Title |
Control, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Suv39h1+/y Suv39h2+/-
gender: Male
cell type: CD4+CD8+ double positive thymocytes
background strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with formaldehyde as described by Rao et al (Cell 2014; PMID: 25497547).
In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547). In situ Hi-C libraries were sequenced on an Illumina NextSeq 500 to produce paired-end 81bp reads.
|
| |
|
| 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 v1.9.1.
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 supplementary 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 |
Aug 14, 2020 |
| Last update date |
Mar 28, 2024 |
| 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 (2) |
| GSE156294 |
in situ Hi-C profiles of DP thymocyltes from control and Suv39h1/Suv39h2 double knockout mice |
| GSE156297 |
RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice |
|
| Relations |
| BioSample |
SAMN15824126 |
| SRA |
SRX8949752 |
