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Series GSE135560 Query DataSets for GSE135560
Status Public on Aug 14, 2019
Title Profiling of PML-body associated regions
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address functional roles of the PML-chromatin association, we conducted genome-wide profiling of PML body-associated regions.
Overall design We performed genome-wide profiling of genomic regions associated with PML bodies in mESCs. Cells were treated with H2O2 to trigger labeling of chromatin with biotin (H2O2+). Experimental negative controls (H2O2-), where the H2O2 treatment was omitted, were also analyzed. Sequence reads were trimmed by using Trimmomatic, then mapped to repeat masked mm10 using bowtie2 version with parameter -N1. ENCODE blacklisted regions and grey list prepared by chipseq-greylist were subsequently removed using bedtools.
BigWig files were generated by using bamCompare with option --scaleFactorsMethod SES --operation subtract.

Contributor(s) Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y
Citation(s) 32353257
Submission date Aug 08, 2019
Last update date Nov 22, 2023
Contact name Misuzu Kurihara
Organization name National Institute for Basic Biology
Street address 5-1 Higashiyama, Myodaiji
City Okazaki
State/province Aichi
ZIP/Postal code 444-8787
Country Japan
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (4)
GSM4017172 ESCs, ALaP_H2O2-_rep1
GSM4017173 ESCs, ALaP_H2O2-_rep2
GSM4017174 ESCs, ALaP_H2O2+_rep1
This SubSeries is part of SuperSeries:
GSE135563 Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions
BioProject PRJNA559288
SRA SRP217815

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 284.3 Mb (ftp)(http) BW
GSE135560_ALaPseq.replicateMERGEDpeaks.bed.gz 212.0 Kb (ftp)(http) BED 284.3 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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