|
| Status |
Public on Sep 29, 2023 |
| Title |
MCP 43 tom+ tumor cells |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted Tomato positive tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: FACS sorted Tomato positive tumor cells
genotype: Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumors were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
Libraries were prepared using the Arima-HiC Kit (#A510008, Arima Genomics)
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end reads of 150 bp reads were processed by Juicer (v1.5, default parameters) based on mm10 and Arima fragment (cut sites GATC or GANTC).
Each replicate was processed separately using default parameters (every replicate got > 500M pairs as > 360M contacts). We required MAPQ score greater than 30 for generating .hic file and downstream analysis.
Loops were called by HiCCUPS from Juicer package (default parameters). Reproducibility have been confirmed by visual inspection.
Assembly: mm10(GRCm38.p6)
Supplementary files format and content: hic file
|
| |
|
| Submission date |
Nov 17, 2022 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE218254 |
PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity[Hi-C] |
| GSE218274 |
PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity |
|
| Relations |
| BioSample |
SAMN31776240 |
| SRA |
SRX18298884 |
