GSM2741765: ZNF711 ChIP-seq in MCF7 rep2; Homo sapiens; ChIP-Seq - SRA

SRX3091905: GSM2741765: ZNF711 ChIP-seq in MCF7 rep2; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 45.2M spots, 2.2G bases, 868.8Mb downloads

Submitted by: NCBI (GEO)

Study: 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

PRJNA398222 • SRP115395 • All experiments • All runs

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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

Sample: ZNF711 ChIP-seq in MCF7 rep2

SAMN07503521 • SRS2429251 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: Illumina HiSeq 3000

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: For RNA-seq, RNA was extracted using Trizol reagent (15596-026) (Life technologies, Carlsbad, CA) following its protocol. For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For NOMe-seq, after isolating nuclei from the cells, M.CviPI was treated to methylate accessible GpCs. After purifying M.CvPI-treated DNA, sonication was performed. Bisulfite treatment of M.CviPI-methylated DNA resulted to convert all unmethylated Cs to Ts. RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA). ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX). NOMe-seq: Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms.

Experiment attributes:

GEO Accession: GSM2741765

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 45.2M spots, 2.2G bases, 868.8Mb

Run	# of Spots	# of Bases	Size	Published
SRR5931660	45,218,156	2.2G	868.8Mb	2018-01-25

ID:: 4381610

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