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Series GSE102616 Query DataSets for GSE102616
Status Public on Jan 24, 2018
Title ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary We performed ChIP-seq in four cancer cell lines to identify ZFX binding sites throughout the human genome. We also performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucelosome, suggesting that ZFX may play a critical role in promoter architecture. We also showed that ZNF711 may function redundantly with ZFX in MCF7 by performing ZNF711 ChIP-seq and RNA-seq analysis after knockdown of ZFX, ZNF711, and both ZFX and ZNF711.
Overall design ChIP-seq, NOMe-seq and RNA-seq
Contributor(s) Rhie S, Yao L, Witt H, Luo Z, Schreiner S, Guo Y, Perez A, Farnham P
Citation(s) 29429977, 31515496
Submission date Aug 14, 2017
Last update date Oct 25, 2022
Contact name Suhn K Rhie
Organization name University of Southern California
Street address 1450 Biggy Street
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (47)
GSM2741762 ZFX ChIP-seq in MCF7 rep1
GSM2741763 ZFX ChIP-seq in MCF7 rep2
GSM2741764 ZNF711 ChIP-seq in MCF7 rep1
BioProject PRJNA398222
SRA SRP115395

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Supplementary file Size Download File type/resource
GSE102616_C42B_H3K4me3_ChIP.bedGraph.gz 19.4 Mb (ftp)(http) BEDGRAPH
GSE102616_C42B_NDR.txt.gz 3.6 Mb (ftp)(http) TXT
GSE102616_C42B_POLR2A_ChIP.bedGraph.gz 6.5 Mb (ftp)(http) BEDGRAPH
GSE102616_C42B_ZFX_ChIP_peaks.txt.gz 222.1 Kb (ftp)(http) TXT
GSE102616_C42B_siZFX_experiment_gene_counts.txt.gz 629.9 Kb (ftp)(http) TXT
GSE102616_HCT116_ZFX_ChIP_peaks.txt.gz 240.3 Kb (ftp)(http) TXT
GSE102616_HEK293T_ZFX_ChIP_peaks.txt.gz 230.1 Kb (ftp)(http) TXT
GSE102616_MCF7_ZFX_ChIP_peaks.txt.gz 240.6 Kb (ftp)(http) TXT
GSE102616_MCF7_ZNF711_ChIP_peaks.txt.gz 104.1 Kb (ftp)(http) TXT
GSE102616_MCF7_siZFX_experiment_gene_counts.txt.gz 594.8 Kb (ftp)(http) TXT
GSE102616_MCF7_siZNF711_siZFX_siBoth_experiment_gene_counts.txt.gz 1.0 Mb (ftp)(http) TXT
GSE102616_PrEC_ZFX_ChIP_peaks.txt.gz 136.6 Kb (ftp)(http) TXT
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