|
| Status |
Public on Dec 12, 2021 |
| Title |
HCI005 Vehicle 3 ER |
| Sample type |
SRA |
| |
|
| Source name |
HCI005 Vehicle tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer PDX model HCI006
treatment: Vehicle
replicate: 3
chip antibody: ER (Millipore SC-543X)
|
| 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 |
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for ER and FOXA1 ChIP-seq experiments. Using a cryostat (Leica, #CM3050-S), 15x 30 µm sections were cut from each tumour at -20 ̊C and these samples were subjected to double fixation with DSG and formaldehyde as previously described (Singh et al., 2019).
Library preparation for ChIP-Seq was performed using the QIAseq Ultralow Input Library Kit (Qiagen, #180495).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-seq reads were aligned against human genome (hg38/GRCh38) using bowtie2 with default parameters.
Peak calling of individual ChIP–seq experiments was performed with MACS2 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: narrowpeak files contain peaks generated using Macs2 (FDR < 55).
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Dec 12, 2021 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
j.achinger@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Lab |
Epigenetics Research Laboratory
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE171070 |
Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [ChIP-seq] |
| GSE171074 |
The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer |
|
| Relations |
| BioSample |
SAMN18527284 |
| SRA |
SRX10468626 |
