|
| Status |
Public on Jan 20, 2023 |
| Title |
priB_TriC_B18AIDKO_Emucapture_0h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
primary B-cells
|
| Organism |
Mus musculus |
| Characteristics |
capture probe: Emu capture
treatment: WT
clone: clone 1
replicate: replicate 2
|
| Growth protocol |
Complete RPMI medium with LPS and IL4 for activation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Tri-C
|
| Data processing |
Library strategy: Tri-C
Tri-C
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: mm9
Supplementary files format and content: Tab separated matrix showing normalized interaction counts
|
| |
|
| 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) |
| GSE198179 |
A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination [Tri-C] |
| GSE198182 |
A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination |
|
| Relations |
| BioSample |
SAMN26537412 |
| SRA |
SRX14412889 |
