|
| Status |
Public on Aug 07, 2019 |
| Title |
Investigation of bivalently marked promoters in patient-derived colorectal cancer stem cells by ChIP-seq, chromatin accessibility by ATAC-seq, and differential regulation of gene expression following EZH2 inhibition using RNA-seq. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We profiled changes in gene expression following EZH2 inhibition, in a patient-derived, cancer stem cell enriched model. Cells were treated with UNC1999, an EZH2 inhibitor, for 7 days, prior to processing for RNA-seq. In parallel, we identified H3K27me3 and H3K4me3 marked promoters using ChIP-seq at baseline in the same model, as well as chromatin accessibility using ATAC-seq.
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| Overall design |
Colorectal cancer stem cells were profiled for bivalently marked (H3K4me3), repressed (H3K27me3) and active (H3K4me3) promoters at baseline. Cells were treated with the EZH2 inhibitor UNC1999, and processed for RNA-seq. ChIP-seq data was used to determine whether the promoters of the differentially regulated genes were marked with repressive, active or bivalent marks. ATAC-seq was performed at baseline to determine chromatin accessibility and used for transcription factor motif analysis.
Raw data will be submitted to EGA due to patient privacy concerns.
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| Contributor(s) |
Lima-Fernandes E, da Silva Medina T, Murison A |
| Citation(s) |
30926792 |
| |
| Submission date |
Apr 16, 2018 |
| Last update date |
Aug 07, 2019 |
| Contact name |
Alexander James Murison |
| E-mail(s) |
alexander.murison@uhnresearch.ca
|
| Organization name |
University Health Network
|
| Lab |
Dick Lab
|
| Street address |
101 College Street, TMDT room 11-706
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA450375 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE113176_All_Genes.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE113176_D0_Suspension_Untreated_H3K4me3_1.hg19.sorted.dedup.q30.bamMACS2_peaks.narrowPeak.gz |
953.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE113176_D0_Suspension_Untreated_H3K4me3_2.hg19.sorted.dedup.q30.bamMACS2_peaks.narrowPeak.gz |
901.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE113176_SUS_1_Day_0_ATAC_TAAGGCGA_L001_R1.fastq.gz.output.hg19.sorted.dedup.q30.bam.MACS_peaks.narrowPeak.gz |
468.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE113176_SUS_2_Day_0_ATAC_CGTACTAG_L001_R1.fastq.gz.output.hg19.sorted.dedup.q30.bam.MACS_peaks.narrowPeak.gz |
427.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE113176_SUS_3_Day_0_ATAC_TCCTGAGC_L001_R1.fastq.gz.output.hg19.sorted.dedup.q30.bam.MACS_peaks.narrowPeak.gz |
427.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE113176_Sus_1_BROAD_H3K27me3_peaks.broadPeak.gz |
3.7 Mb |
(ftp)(http) |
BROADPEAK |
| GSE113176_Sus_2_BROAD_H3K27me3_peaks.broadPeak.gz |
1.8 Mb |
(ftp)(http) |
BROADPEAK |
| Raw data not provided for this record |
| Processed data are available on Series record |
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