GSE112439
GSE GEOThe RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RRBS]
Organism:
Homo sapiens
Platform:
GPL16791
Samples:
2
Experiment Types:
Methylation profiling by high throughput sequencing
Submitted:
Mar 28 2018
Last Updated:
Oct 16 2019
Status:
Public on Oct 16 2019
Contact:
Kendell,,Clement (Harvard University)
Relations
SubSeries of: GSE112479
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA446040
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP136635
Summary
Analysis of human embryonic stem cells and induced pluripotent 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
Human induced pluripotent stem cells depleted for DDX6.
Analysis (4 steps)
View Data Processing
Processing steps for GSE112439
- Preprocessing: 10bp were trimmed from the beginning of each read to remove possible adapter contamination
- Alignment: Reads were aligned using Bsmap with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8 -
- Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read.
- If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Supplementary Files (1)
GSE112439_RAW.tar
Download
GEO Samples (2)
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 (8)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | ESC_sgCTRL.1.R1.fq.gz | Bisulfite-Seq | 661.0 MB | link | |||
| — | ESC_sgCTRL.2.R1.fq.gz | Bisulfite-Seq | 631.9 MB | link | |||
| — | ESC_sgCTRL.3.R1.fq.gz | Bisulfite-Seq | 629.7 MB | link | |||
| — | ESC_sgCTRL.4.R1.fq.gz | Bisulfite-Seq | 614.6 MB | link | |||
| — | ESC_sgDDX6.1.R1.fq.gz | Bisulfite-Seq | 461.4 MB | link | |||
| — | ESC_sgDDX6.2.R1.fq.gz | Bisulfite-Seq | 440.9 MB | link | |||
| — | ESC_sgDDX6.3.R1.fq.gz | Bisulfite-Seq | 447.1 MB | link | |||
| — | ESC_sgDDX6.4.R1.fq.gz | Bisulfite-Seq | 436.4 MB | link |