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Series GSE135562 Query DataSets for GSE135562
Status Public on Aug 14, 2019
Title ChIP-seq analysis of 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 roles of PML bodies in transcriptional regulation, we conducted ChIP-seq analysis for histone modifications, including H3K4me3, H3K27ac, H3K27me3, and H3K9ac with wild-type and PML knockout mESCs.
 
Overall design 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 XS tag. 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
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Submission date Aug 08, 2019
Last update date Aug 14, 2019
Contact name Misuzu Kurihara
E-mail(s) kmisuzu1018@gmail.com
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 (18)
GSM4017180 ESCs, WT_ChIP_H3K27ac_rep1
GSM4017181 ESCs, WT_ChIP_H3K27ac_rep2
GSM4017182 ESCs, PmlKO_ChIP_H3K27ac_rep1
This SubSeries is part of SuperSeries:
GSE135563 Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions
Relations
BioProject PRJNA559289
SRA SRP217817

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135562_ChIPseq.H3K27ac.mESC_PMLKO.RPKM.mm10.bw 160.2 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K27ac.mESC_WT.RPKM.mm10.bw 137.5 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K27me3.mESC_PMLKO.RPKM.mm10.bw 200.9 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K27me3.mESC_WT.RPKM.mm10.bw 220.2 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K4me3.mESC_PMLKO.RPKM.mm10.bw 112.3 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K4me3.mESC_WT.RPKM.mm10.bw 118.7 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K9me3.mESC_PMLKO.RPKM.mm10.bw 157.3 Mb (ftp)(http) BW
GSE135562_ChIPseq.H3K9me3.mESC_WT.RPKM.mm10.bw 167.9 Mb (ftp)(http) BW
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