|
| Status |
Public on Sep 14, 2018 |
| Title |
Epigenetic and transcriptional profiling of triple negative breast cancer |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The human HCC1806 cell line is frequently used as a preclinical model for triple negative breast cancer (TNBC). Given that dysregulated epigenetic mechanisms are involved in cancer pathogenesis, emerging therapeutic strategies target chromatin regulators, such as histone deacetylases. A comprehensive understanding of the epigenome and transcription profiling in HCC1806 provides the framework for evaluating efficacy and molecular mechanisms of epigenetic therapies. Thus, to study the interplay of transcription and chromatin in the HCC1806 preclinical model, we performed nascent transcription profiling using Precision Run-On coupled to sequencing (PRO-seq). Additionally, we mapped the genome-wide locations for RNA polymerase II (Pol II), CTCF, the histone variant H2A.Z, and 7 histone modifications using ChIP-exo. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq with near base pair precision mapping of protein-DNA interactions. In this Data Descriptor, we present detailed information on experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the nascent transcription and chromatin.
|
| |
|
| Overall design |
We performed nascent transcription profiling using Precision Run-On coupled to sequencing (PRO-seq). Additionally, we mapped the genome-wide locations for RNA polymerase II (Pol II), CTCF, the histone variant H2A.Z, and 7 histone modifications using ChIP-exo. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq with near base pair precision mapping of protein-DNA interactions.
|
| |
|
| Contributor(s) |
Perreault AA, Walheim DM, Venters BJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA483476 |
| Submission date |
Aug 02, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Andrea Perreault |
| E-mail(s) |
andrea.a.perreault@vanderbilt.edu
|
| Phone |
9083045070
|
| Organization name |
Vanderbilt University
|
| Street address |
746 Robinson Research Building
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (22)
|
| GSM3317509 |
1-ChIP-exo of HCC1806 cells: CTCF |
| GSM3317510 |
1-ChIP-exo of HCC1806 cells: modification H3K4me3 |
| GSM3317511 |
1-ChIP-exo of HCC1806 cells: modification H3K4me2 |
| GSM3317512 |
1-ChIP-exo of HCC1806 cells: modification H3K4me1 |
| GSM3317513 |
1-ChIP-exo of HCC1806 cells: modification H3K27ac |
| GSM3317514 |
1-ChIP-exo of HCC1806 cells: modification H3K27me3 |
| GSM3317515 |
1-ChIP-exo of HCC1806 cells: modification H3K9ac |
| GSM3317516 |
1-ChIP-exo of HCC1806 cells: modification H4K20me1 |
| GSM3317517 |
2-PRO-seq of HCC1806 cells |
| GSM3317518 |
2-ChIP-exo of HCC1806 cells: RNA polymerase II |
| GSM3317519 |
2-ChIP-exo of HCC1806 cells: histone H2AZ |
| GSM3317520 |
2-ChIP-exo of HCC1806 cells: CTCF |
| GSM3317521 |
2-ChIP-exo of HCC1806 cells: modification H3K4me3 |
| GSM3317522 |
2-ChIP-exo of HCC1806 cells: modification H3K4me2 |
| GSM3317523 |
2-ChIP-exo of HCC1806 cells: modification H3K4me1 |
| GSM3317524 |
2-ChIP-exo of HCC1806 cells: modification H3K27ac |
| GSM3317525 |
2-ChIP-exo of HCC1806 cells: modification H3K27me3 |
| GSM3317526 |
2-ChIP-exo of HCC1806 cells: modification H3K9ac |
| GSM3317527 |
2-ChIP-exo of HCC1806 cells: modification H4K20me1 |
|
| Relations |
| SRA |
SRP155750 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE118033_CTCF-AP_ChIP-exo_merge.b20s100dt.bw |
250.7 Mb |
(ftp)(http) |
BW |
| GSE118033_DMSO_PRO-seq_merge.b20s100dt.bw |
189.4 Mb |
(ftp)(http) |
BW |
| GSE118033_H2A.Z_ChIP-exo_merge.b20s100dt.bw |
336.0 Mb |
(ftp)(http) |
BW |
| GSE118033_H3K27Ac_ChIP-exo_merge.b20s100dt.bw |
379.8 Mb |
(ftp)(http) |
BW |
| GSE118033_H3K27me3_ChIP-exo_merge.b20s100dt.bw |
333.9 Mb |
(ftp)(http) |
BW |
| GSE118033_H3K4me1_ChIP-exo_merge.b20s100dt.bw |
507.1 Mb |
(ftp)(http) |
BW |
| GSE118033_H3K4me2_ChIP-exo_merge.b20s100dt.bw |
330.5 Mb |
(ftp)(http) |
BW |
| GSE118033_H3K4me3_ChIP-exo_merge.b20s100dt.bw |
424.3 Mb |
(ftp)(http) |
BW |
| GSE118033_H3K9Ac_1727-3194_ChIP-exo_merge.b20s100dt.bw |
145.9 Mb |
(ftp)(http) |
BW |
| GSE118033_H4K20me1_ChIP-exo_merge.b20s100dt.bw |
625.2 Mb |
(ftp)(http) |
BW |
| GSE118033_Pol-II_ChIP-exo_merge.b20s100dt.bw |
375.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...