|
| Status |
Public on Jun 09, 2023 |
| Title |
CAF culture from mouse # 66383 pcMicro-C replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
pcMicro-C in cultured cancer-associated fibroblasts 30 minutes after serum stimulation
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Serum-starved and stimulated cultured CAF
genotype: dKO
assay: pcMicro-C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10^6 short-term cultured CAFs after 30min serum stimulation were processed for Micro-C was performed using the Dovetail Micro-C Kit (Cantata Bio) according to the manufacturer’s protocol. Chromatin from 1 × 106 WT and dKO cultured CAFs, cross-linked after serum stimulation, was digested with 3 μl MNAse to obtain a mononucleosomal fraction within specifications.
Each chromatin preparation was subjected to proximity ligation and subsequent library preparation in duplicate. 400 ng of each library was pooled and subjected to promoter capture using the Dovetail Target Enrichment Kit and Mouse Pan Promoter Panel (Cantata Bio).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
dKO_merged_10k_loops.bigInteract
|
| Data processing |
library strategy: pcMicro-C
Interaction calling and significance thresholding was performed based on the workflow developed by Dovetail Genomics (https://micro-c.readthedocs.io/en/latest/) and the CHiCAGO tool recommendations. Sequenced reads were aligned using BWA v0.7.17-r1188 and filtered using PairTools v1.0.2 and SAMTools v1.9 to identify non-duplicated read-pairs. The technical replicates were merged, and significant interactions (chromatin loops) were called using CHiCAGO v1.2.0 with default parameters at 10kb resolution. Significant Interactions were defined as those with a CHiCAGO score ≥ 5 per condition.
For visualization on the UCSC Genome Browser, output loop files were converted from WashU EpiGenome Browser interactBED format to bigInteract format using BEDTools v2.30.0 and UCSC-Utils v2.9.
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: bigInteract - aligned reads pileup produced with deeptools
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Dan Filipescu |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Oncological Sciences
|
| Lab |
Emily Bernstein
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE200751 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts. |
| GSE229531 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts [3D chromatin] |
|
| Relations |
| SRA |
SRX19947981 |
| BioSample |
SAMN34159592 |
