|
| Status |
Public on Jul 24, 2023 |
| Title |
Gar15-13 Decitabine 1 CTCF |
| Sample type |
SRA |
| |
|
| Source name |
Gar15-13 Decitabine tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer PDX model Gar15-13
treatment: Decitabine
replicate: 1
chip antibody: CTCF (Millipore-Merck 07-729)
|
| 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.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for CUT&RUN experiments using Epicypher CUTANA ChIC/CUT&RUN Kit (Cat#14-1048) and CUTANA CUT&RUN Library Prep Kit (Primer Set 1) (Cat#14-1001).
Library preparation for CUT&RUN was performed using the Epicypher CUTANA CUT&RUN Library Prep Kit (Primer Set 1) (Cat#14-1001).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
CUT&RUN reads were aligned against human genome (hg38/GRCh38) using bowtie2 with --dovtail parameters, sorted with samtools and duplicates were marked with picard.
Peak calling of individual CUT&RUN experiments was performed with MACS2.
Assembly: hg38
Supplementary files format and content: narrowpeak and broadpeak files contain peaks generated using Macs2 (FDR < 0.05).
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Jul 19, 2023 |
| Last update date |
Jul 24, 2023 |
| 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 |
GPL18573 |
| Series (2) |
| GSE171074 |
The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer |
| GSE237769 |
Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer [CUT&RUN] |
|
| Relations |
| BioSample |
SAMN36632511 |
| SRA |
SRX21084701 |
