|
| Status |
Public on Aug 07, 2023 |
| Title |
TAMR Decitabine Day 7 1 [PCHi-C] |
| Sample type |
SRA |
| |
|
| Source name |
TAMR cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tamoxifen-resistant (TAMR) MCF7 cells
treatment: Decitabine Day 7
replicate: 1
|
| Treatment protocol |
Cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control Early”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35. Matched control cells were cultured for 35 days in normal media and harvested at day 35 for “Control Late”.
|
| Growth protocol |
Tamoxifen-resistant MCF7 cells (TAMR) were previously generated by the long-term culture of MCF7 cells in phenol red-free RPMI medium containing 10% charcoal-stripped FBS (Gibco) and 4-OH-tamoxifen (1 × 10−7 M; TAM).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiments were performed on fresh-frozen tumour samples using the Arima Hi-C+ kit (Arima Genomics, Inc.) with minor modifications. Hi-C libraries were then used for Promoter Capture enrichment.
PCHi-C libraries were prepared using the SureSelect target enrichment system (SureSelect XT HS2 DNA kit, Agilent Technologies) using custom-design RNA bait library.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TAMR_Aza_D7_Rep_1
|
| Data processing |
PCHi-C sequenced reads were mapped and filtered using HiCUP (v.0.7.4) (Wingett et al., 2015) with hg38/GRCh38 genome digested with –arima flag and minimum di-tag length set to 20.
Unique, valid mapped reads from HiCUP were converted into .chinput files using bam2chicago.sh utility and obtained chinput files were further filtered and processed with CHiCAGO (v.1.14.0)
Assembly: GRCh38/hg38
Supplementary files format and content: chinput files containing unique, valid mapped reads.
|
| |
|
| Submission date |
Nov 01, 2022 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
j.achinger@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE216987 |
Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [Promoter Capture Hi-C] |
| GSE216989 |
Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions |
|
| Relations |
| BioSample |
SAMN31556328 |
| SRA |
SRX18108896 |
