GSE125954
GSE GEOThe RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ChIP-Seq]
Organism:
Homo sapiens
Platform:
GPL18573
Samples:
6
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted:
Jan 31 2019
Last Updated:
Oct 16 2019
Status:
Public on Oct 16 2019
Contact:
Jocelyn,,Charlton (Harvard University)
Relations
SubSeries of: GSE112479
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA518086
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP183182
Summary
Analysis of adult and embryonic stem cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6.
Overall Design
ChIP-seq
Analysis (4 steps)
View Data Processing
Processing steps for GSE125954
- Reads were trimmed using cutadapt and aligned to the hg19 genome using BWA.
- Duplicate reads were marked using picard tools, and reads were filtered for a mapq score > 15.
- Macs2 callpeak was used to call peaks, with --broad used for H3K9me3.
- To generate peak sets, macs2 called peaks were extended by 500bp then only kept if present and overlapping in both biological replicates.
Supplementary Files (1)
GSE125954_RAW.tar
Download
GEO Samples (6)
Dataset Citations (1)
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
PMID 31588046
· 2019
· Cell stem cell
Bruno Di Stefano, En-Ching Luo, Chuck Haggerty, Stefan Aigner, Jocelyn Charlton, Justin Brumbaugh, Fei Ji, Inés Rabano Jiménez, Katie J Clowers, Aaron J Huebner, Kendell Clement, Inna Lipchina, Marit A C de Kort, Anthony Anselmo, John Pulice, Mattia F M Gerli, Hongcang Gu, Steven P Gygi, Ruslan I Sadreyev, Alexander Meissner, Gene W Yeo, Konrad Hochedlinger
Linked Publications (1)
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019
Data Files (10)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | CTRL_H3K27ac_rep1.bam | ChIP-Seq | 162.8 MB | link | |||
| — | CTRL_H3K27ac_rep2.bam | ChIP-Seq | 177.2 MB | link | |||
| — | CTRL_H3K9me3_rep1.bam | ChIP-Seq | 92.0 MB | link | |||
| — | CTRL_H3K9me3_rep2.bam | ChIP-Seq | 257.7 MB | link | |||
| — | DDX6_H3K27ac_rep1.bam | ChIP-Seq | 136.4 MB | link | |||
| — | DDX6_H3K27ac_rep2.bam | ChIP-Seq | 223.0 MB | link | |||
| — | DDX6_H3K4me3_rep1.bam | ChIP-Seq | 113.2 MB | link | |||
| — | DDX6_H3K4me3_rep2.bam | ChIP-Seq | 150.6 MB | link | |||
| — | DDX6_H3K9me3_rep1.bam | ChIP-Seq | 87.4 MB | link | |||
| — | DDX6_H3K9me3_rep2.bam | ChIP-Seq | 244.5 MB | link |