|
| Status |
Public on Apr 14, 2020 |
| Title |
Erg KO rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived B220+ B-cell progenitors
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C56BL/6
genotype: Rag1CreT/+;Erg fl/fl (Erg KO)
gender: female
cell type: B-cell progenitor
|
| Treatment protocol |
Lineage negative bone marrow was cultured for 8 days on OP9 stromal cells with SCF, IL7 and FL cytokines, and purified using B220 positive selection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547).
DNA was sequenced on an Illumina NextSeq 500 to produce 80bp paired-end reads using standard Illumina protocols.
|
| |
|
| 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 100 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 100 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 |
Jun 24, 2019 |
| Last update date |
Apr 15, 2020 |
| 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) |
| GSE133246 |
Hi-C profiling of B-cell progenitors from Erg KO and WT mice |
|
| Relations |
| BioSample |
SAMN12129672 |
| SRA |
SRX6358314 |
