|
| Status |
Public on Sep 11, 2009 |
| Title |
ERα_ChIP-PET (454) |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
library: ChIP-PET
|
| Treatment protocol |
In preparation for the 17 beta-estradiol (“estrogen”, E2, Sigma) treatment, cells were grown in hormone-free media: they were washed with PBS and incubated in phenol red-free medium (Invitrogen/Gibco) supplemented with 5% charcoal-dextran stripped FBS (Hyclone), penicillin, streptomycin, gentamycin, and L-glutamine (Invitrogen) for a minimum of 72 hours. Hormone-depleted cells were treated with estrogen to a final concentration of 100 nM for 45 min before the ChIP procedure.
|
| Growth protocol |
MCF-7 cells were grown to at least 80% confluence in DMEM/F12 (Invitrogen/Gibco) supplemented with 5% FBS (Invitrogen/Gibco), penicillin (Invitrogen), streptomycin (Invitrogen), and gentamycin (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We used 1% formaldehyde to crosslink the cells, and sonication to break the chromatin fibers. Antibodies were used to enrich chromatin fragments by ChIP. After this either ChIA-PET or ChIP-Seq was performed.
|
| |
|
| Library strategy |
ChIA-PET |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
454 GS FLX |
| |
|
| Description |
A control ChIP-PET library against ERα in MCF-7 human breast cancer cells in estrogen-treated condition.
|
| Data processing |
Mapping analysis was performed by Compressed Suffix Arrays and results were further processed using the ChIA-PET pipeline software.
|
| |
|
| Submission date |
Sep 11, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Ruan |
| E-mail(s) |
ruanyj@gis.a-star.edu.sg
|
| Phone |
65 6478 8073
|
| URL |
http://www.gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Department |
Research Computing Group
|
| Street address |
60 Biopolis Street, #02-01 Genome, Singapore 138672
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL9186 |
| Series (1) |
| GSE18046 |
An Estrogen Receptor α-bound Human Chromatin Interactome |
|
| Relations |
| SRA |
SRX016697 |
| BioSample |
SAMN00008905 |
