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| 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
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| 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.
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| 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 2.3.5.1 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.
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| 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 |
| E-mail(s) |
kmisuzu1018@gmail.com, miyanari@nibb.ac.jp
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| Organization name |
National Institute for Basic Biology
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| Street address |
5-1 Higashiyama, Myodaiji
|
| City |
Okazaki |
| State/province |
Aichi |
| ZIP/Postal code |
444-8787 |
| Country |
Japan |
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| Platforms (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE135563 |
Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions |
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| Relations |
| BioProject |
PRJNA559288 |
| SRA |
SRP217815 |
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