|
| Status |
Public on Aug 31, 2022 |
| Title |
HiChIP-MCF7 |
| Sample type |
SRA |
| |
|
| Source name |
Breast carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7 breast carcinoma cell line
agent: Estrogen
chip antibody: H3K27ac (C15410196, Diagenode)
|
| Treatment protocol |
Cells were treated with 10nM E2 for 45 minutes
|
| Growth protocol |
Cells were grown in estrogen deprived media for 3 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After proximity ligation with biotin-dATP, nuclei were lysed and sonicated and chromatin immunoprecipitation with H3K27AC, followed by DNA purification and biotin capture of the Hi-C contacts
DNA library preparation was performed with Tn5 on beads, amplifying for 11 cycles total
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: Hi-ChIP
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using hic-pro and fithichip
|
| |
|
| Submission date |
Jun 12, 2020 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Rinath Jeselsohn |
| Organization name |
DFCI
|
| Department |
Medical Oncology
|
| Lab |
Jeselsohn Lab
|
| Street address |
450 Brookline Ave, D728
|
| City |
Boston |
| State/province |
MD |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE152366 |
FOXA1 Shapes the Chromatin State of ILC and Drives Differential Response to Aromatase Inhibitors and Tamoxifen [HiChIP-seq] |
| GSE152367 |
Chromatin Accessibility differentiates Invasive Lobular from Invasive Ductal Breast cancer and Dictates Response to Endocrine Treatment |
|
| Relations |
| BioSample |
SAMN15223341 |
| SRA |
SRX8537762 |
