|
| Status |
Public on Nov 08, 2019 |
| Title |
Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using ChIP-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2-HA protein. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 3 treatments (Veh, Dox, DoxTam) were performed in duplicates. After treatments, cells were collected for ChIP experiment with HA antibody. ChIP-seq libraries were sequenced and data analysis showed almost no binding in Veh treatment, indicating low backgroud and good quality of the data. PAX transcription factor motif were enriched in PAX2 peaks, indicating the reliability of the data. When crossing the ChIP-seq data with genes regulated by PAX2 in MCF-7, we could observe high level binding of PAX2 to prmoters of PAX2 up-regulated genes and the center of intergenic transcripts induced by PAX2, suggesting the role of PAX2 in regulating transcription activation.
|
| |
|
| Overall design |
PAX2 genome interaction mapping in MCF-7 cells treated with doxycycline (50ng/ml) alone, or in combination with tamoxifen (1uM). Whole experiment include 2 replicates of each treatments, a Veh control (no PAX2-HA overexpression), and input samples.
|
| |
|
| Contributor(s) |
Wang S, Chernukhin I, Carroll JS, Hurtado A |
| Citation(s) |
32843722 |
| |
| Submission date |
Nov 07, 2019 |
| Last update date |
Oct 26, 2020 |
| Contact name |
Shixiong Wang |
| E-mail(s) |
[email protected]
|
| Phone |
+47-22845865
|
| Organization name |
University of Oslo
|
| Department |
Centre for Molecular Medicine Norway
|
| Street address |
Gaustadalléen 21
|
| City |
Oslo |
| ZIP/Postal code |
0349 |
| Country |
Norway |
| |
|
| Platforms (2) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (7)
|
|
| Relations |
| BioProject |
PRJNA588153 |
| SRA |
SRP229065 |
Less...
More...