|
| Status |
Public on May 01, 2021 |
| Title |
Prostate-DU145-HiC-1 |
| Sample type |
SRA |
| |
|
| Source name |
DU145 cells (ATCC HTB-81). Brain metastatic prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DU145
source tissue/cell type: Brain metastatic prostate cancer
condition: Cells grown under control conditions
media: DMEM, 10%FBS, 100 g/ml penicillin-streptomycin.
|
| Biomaterial provider |
ATCC HTB-81
|
| Treatment protocol |
Cells were collected from T75 flasks at 80% confluency, under normal growth conditions.
|
| Growth protocol |
All cell lines maintained and split according to ATCC SOPs. MDA Cells grown on FCN Coting Mix (Athena), used according to the manufacturer's instructions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed using the Arima Hi-C (Arima Genomics) kit, or according to established protocols (Goloshi. et.al doi: 10.1016/j.ymeth.2018.04.033)
Manufacturer’s protocol A160141 v01 for library amplification from Arima was used along the NEBNext Ultra II kit (NEB E7645S).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DU145-60
|
| Data processing |
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github
Iterative correction was performed using method described by Imakaev et al.
Genome_build: hg19
Supplementary_files_format_and_content: Each .tar file contains the iteratively corrected and raw matrix.gz files for 20 kb, 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories. Bin size indicated as “C-40000” for example. All matrices are for individual chromosomes except for the 2.5 Mb bin size
|
| |
|
| Submission date |
Apr 14, 2021 |
| Last update date |
May 02, 2021 |
| Contact name |
Rebeca SanMartin |
| E-mail(s) |
rsanmart@utk.edu
|
| Organization name |
University of Tennessee Knoxville
|
| Street address |
1311 Cumberland Avenue
|
| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE172097 |
Alterations in chromosome spatial compartmentalization classify prostate cancer progression [Hi-C] |
| GSE172099 |
Alterations in chromosome spatial compartmentalization classify prostate cancer progression. |
|
| Relations |
| BioSample |
SAMN18742590 |
| SRA |
SRX10602636 |
