|
| Status |
Public on Jan 20, 2023 |
| Title |
priB_MicroC_Spt5depleted |
| Sample type |
SRA |
| |
|
| Source name |
primary B-cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: control
|
| Treatment protocol |
4-hydroxy tamoxifen for 32h
|
| Growth protocol |
Complete RPMI with LPS and IL4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed exactly as in Hsieh et al. (Moleular Cell 2020)
Performed exactly as in Hsieh et al. (Moleular Cell 2020)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Micro-C
|
| Data processing |
Library strategy: Micro-C
Micro-C
Raw sequening reads were processed and aligned to the mm9 reference with the distiller-nf pipeline (https://github.com/open2c/distiller-nf) using default parameters.
In brief, reads were split into smaller chunks, quality and adapter trimmed using fastp and subsequently aligned with the Burrows Wheeler aligner.
Split BAM files were sorted by position, merged, deduplicated with pairtools (https://github.com/open2c/pairtools).
Contact maps in different resolutions were then computed from generated pairs files using cooler commandline tools and balanced using iterative correction.
Assembly: NCBI mm9
Supplementary files format and content: mcool
|
| |
|
| Submission date |
Mar 09, 2022 |
| Last update date |
Jan 23, 2023 |
| Contact name |
Maximilian Christian von der Linde |
| E-mail(s) |
maximilian.linde@imp.ac.at, max_vdl@outlook.com
|
| Phone |
+4368181646556
|
| Organization name |
Institute of Molecular Pathology
|
| Lab |
Pavri GRP
|
| Street address |
Campus-vienna-biocenter 1, IMP, Pavri GRP
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE198181 |
A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination [Micro-C] |
| GSE198182 |
A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination |
|
| Relations |
| BioSample |
SAMN26537419 |
| SRA |
SRX14412956 |
