|
| Status |
Public on Aug 31, 2023 |
| Title |
SpreB-Brwd1KO.1 |
| Sample type |
SRA |
| |
|
| Source name |
Small_Pre-B_cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Small_Pre-B_cell
genotype: BRWD1KO
|
| Treatment protocol |
No treatment was performed
|
| Growth protocol |
No cultured cells were used. All cells used are primary small pre-B cells isolated from bone marrow of WT or BRWD knock out mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C was performed as previously described (Rao Et. al. Cell 2014). Briefly, WT and Brwd1-/- small pre-B and WT immature B cells (5x10^6 for each stage) were crosslinked with 1% formaldehyde following a wash with ice cold PBS. Membranes were lysed to keep nuclei intact followed by restriction digestion with 100U of MboI (NEB R0147). The DNA ends were marked with biotin, ligated proximally and crosslinks were reversed. DNA shearing and size selection were then performed for fragments 300-500 bp. The amount of DNA was quantified with the Qubit dsDNA High Sensitivity Assay (Life technologies, Q32854), and biotin pull down was done to prepare the final in-situ Hi-C libraries (in duplicate).
Libraries were prepered using Immumina Library preparation kit and sequenced on the Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Primary flow purified small pre-B cells from BRWD1 knock-out mouse bone marrow
|
| Data processing |
Hi-C processing was performed using Juicer 6 with default values, aligning to reference genome mm9; MboI fragment sizes were downloaded for mm9 from https://aryeelab.github.io/hichipper/RestrictionFragmentFiles/. Analysis was performed using the juicer.sh pipeline script.
Assembly: mm9
Supplementary files format and content: .hic file from JUICER
|
| |
|
| Submission date |
Dec 21, 2022 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Mark Maienschein-Cline |
| E-mail(s) |
mmaiensc@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Research Resources Center
|
| Lab |
Center for Research Informatics
|
| Street address |
1819 W Polk Ave, Rm 336 M/C 789
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE221517 |
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes (Hi-C) |
| GSE221519 |
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes |
|
| Relations |
| BioSample |
SAMN32352768 |
| SRA |
SRX18809546 |
