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Series GSE135561 Query DataSets for GSE135561
Status Public on Aug 14, 2019
Title ATAC-seq analyses with wild-type and PML KO mESCs
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate functional roles of PML bodies in chromatin organization, we conducted ATAC-seq with wild-type and PML KO mESCs.
Overall design ATAC-seq profile of wild-type and PML-/- mouse embryonic stem cells. Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive. Multiple mapped reads were filtered out using a MAPQ threshold of 30. PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools. bigWig files were generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY
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 May 05, 2020
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)
GSM4017176 ESCs, WT_ATAC_rep1
GSM4017177 ESCs, WT_ATAC_rep2
GSM4017178 ESCs, PmlKO_ATAC_rep1
This SubSeries is part of SuperSeries:
GSE135563 Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions
BioProject PRJNA559287
SRA SRP217816

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