|
| Status |
Public on Sep 05, 2024 |
| Title |
Capture Hi-C in wild type mouse bone marrow derived macrophages |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow-derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
duration of_treatment_(hours): 1
strain: C57BL6
cell type: bone marrow-derived macrophages
genotype: Bach1 fl/fl (control)
treatment: vehicle
|
| Treatment protocol |
Treatments of mouse bone marrow-derived macrophages occurred at Day7 of differentiation after an overnight incubation in fresh medium.
|
| Growth protocol |
Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse bone marrow-derived macrophages were cross-linked using formaldehyde-based cross-linking method and processed to Hi-C using the Arima Hi-C kit. A capture enrichment step was applied to the generated Hi-C libraries using sustom-designed probes (SureSelect, Agilent Tier 2 -2,9Mb ). Our design has two components combined in the same probe set : a. The Hmox1 genomic locus (tiled probescovering a 500kb area). The coordinates of this area arechr8:74850001-75350000. b.9127 sites covering the top BACH1’s ChIP-seqsites (in untreated BMDMs) sorted based on the RPKM.
Hi-C and cHi-C libraries were prepared with the Arima Hi-C kit and Agilent SureSelect library systems according to the manufacturer protocol.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Custom-designed selection probes (SureSelect- Agilent) against BACH1-bound genomic sites
|
| Data processing |
Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Assembly: mm10
Supplementary files format and content: Bigwig file that contain the chromatin interaction frequencies.
|
| |
|
| Submission date |
Sep 05, 2024 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Laszlo Nagy |
| E-mail(s) |
lnagy@jhmi.edu
|
| Organization name |
University of Debrecen
|
| Street address |
Egyetem ter 1.
|
| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE276450 |
Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture |
|
| Relations |
| BioSample |
SAMN43513530 |
| SRA |
SRX25983116 |
