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Series GSE77526 Query DataSets for GSE77526
Status Public on Feb 01, 2020
Title MNase-seq analysis in human breast cancer cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Nucleosomes are the most basic units of chromatin and are regulators of genome integrity and gene expression. The fundamental mechanism how nucleosomes are dynamically regulated is one of the main questions in chromatin organization; most of the study has, however, focused on its positioning. Here we performed HiLo-MNase-seq, which involves limit and partial digestion of chromatin by micrococcal nuclease (MNase) to identify the positioning of nucleosome array along with the kinetics of MNase digestion. We identified a subset of unique nucleosomes with fast digestion kinetics at the transcription factor binding sites that have been characterized as nucleosome depleted regions (NDRs). By inhibiting RNA polymerase II, we also showed that those nucleosomes changed its sensitivity to MNase in a context-dependent manner. These findings implicated a self-reinforcing regulatory network involving nucleosomes, Pol II, and transcription factors for fine-tuning of gene expression.
Overall design MNase-seq experiment was performed in human breast cancer cells, MCF-7. Two biological replicates were prepared.
Contributor(s) Shimbo T, Sara GA, Wade PA
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Submission date Feb 03, 2016
Last update date Feb 02, 2020
Contact name Takashi Shimbo
Organization name NIH/NIEHS
Street address 111 TW Alexander Dr.
City RTP
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (20)
GSM2053642 DMSO_treated_Lo-Mnase_rep_1
GSM2053643 DMSO_treated_Lo-Mnase_rep_2
GSM2053644 FP_treated_Lo-Mnase_rep_1
BioProject PRJNA310726
SRA SRP069236

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Supplementary file Size Download File type/resource
GSE77526_RAW.tar 11.7 Gb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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