|
| Status |
Public on Dec 12, 2021 |
| Title |
Gar15-13 Decitabine 4_PCHiC |
| Sample type |
SRA |
| |
|
| Source name |
Gar15-13 Decitabine tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer PDX model Gar15-13
treatment: Decitabine
replicate: 4
|
| Treatment protocol |
Mice were randomly assigned to treatment groups and treated with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).
|
| Growth protocol |
A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.
|
| 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: PCHi-C
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)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: chinput files containing unique, valid mapped reads.
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Dec 12, 2021 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
[email protected]
|
| Organization name |
South Australian Immunogenomics Cancer Institute
|
| Street address |
AHMS Building, North Terrace
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE171072 |
Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [PCHiC] |
| GSE171074 |
The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer |
|
| Relations |
| BioSample |
SAMN18527937 |
| SRA |
SRX10469153 |
