GSE124071
GSE GEOThe RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ATAC-Seq]
Organism:
Homo sapiens
Platform:
GPL11154
Samples:
8
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted:
Dec 18 2018
Last Updated:
Oct 16 2019
Status:
Public on Oct 16 2019
Contact:
Fei,,Ji (Massachusetts General Hospital)
Relations
SubSeries of: GSE112479
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA510652
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP173836
Summary
Analysis of adult and embryonci 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
ATAC-seq
Analysis (3 steps)
View Data Processing
Processing steps for GSE124071
- Illumina Casava1.7 software used for basecalling.
- Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using BWA
- peaks were called using HOTSPOT with default parameter
Supplementary Files (1)
GSE124071_RAW.tar
Download
GEO Samples (8)
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 (9)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | iPSC.CTRL.1.R1.fastq.gz | ATAC-seq | 2.5 GB | link | |||
| — | iPSC.CTRL.2.R1.fastq.gz | ATAC-seq | 2.4 GB | link | |||
| — | iPSC.DDX6.1.R1.fastq.gz | ATAC-seq | 2.2 GB | link | |||
| — | iPSC.DDX6.2.R1.fastq.gz | ATAC-seq | 2.3 GB | link | |||
| — | Myoblast.CTRL.1.R1.fastq.gz | ATAC-seq | 2.4 GB | link | |||
| — | Myoblast.CTRL.2.R1.fastq.gz | ATAC-seq | 2.0 GB | link | |||
| — | Myoblast.DDX6.1.R1.fastq.gz | ATAC-seq | 2.0 GB | link | |||
| — | Myoblast.DDX6.2.R1.fastq.gz | ATAC-seq | 2.3 GB | link | |||
| — | Myoblast.DDX6.2.R2.fastq.gz | ATAC-seq | 2.3 GB | link |