GSE112383
GSE GEOThe RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq]
Organism:
Homo sapiens
Platform:
GPL11154
Samples:
18
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Mar 27 2018
Last Updated:
Oct 16 2019
Status:
Public on Oct 03 2019
Contact:
Bruno,,Di Stefano (Baylor College of Medicine)
Relations
SubSeries of: GSE112479
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA445858
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP136549
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 embryonic stem cells and induced pluripotent stem cells depleted for DDX6.
Analysis (3 steps)
View Data Processing
Processing steps for GSE112383
- STAR was used to map sequencing reads to human reference genome (Ensembl annotation of hg19 assembly).
- Read counts over transcripts were calculated using HTSeq v.0.6.0 based on Ensembl annotation of hg19 genome.
- Differential expression analysis was performed using EdgeR.
Supplementary Files (3)
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 | |
|---|---|---|---|---|---|---|---|
| — | GEN1C_sgCTRL_TGFBi_rep1.fastq.gz | RNA-Seq | 1.5 GB | link | |||
| — | GEN1C_sgCTRL_TGFBi_rep2.fastq.gz | RNA-Seq | 1.4 GB | link | |||
| — | GEN1C_sgDDX6_TGFBi_rep1.fastq.gz | RNA-Seq | 1.4 GB | link | |||
| — | GEN1C_sgDDX6_TGFBi_rep2.fastq.gz | RNA-Seq | 1.4 GB | link | |||
| — | WIBR3_Naive_rep1.fastq.gz | RNA-Seq | 895.0 MB | link | |||
| — | WIBR3_Naive_rep2.fastq.gz | RNA-Seq | 823.3 MB | link | |||
| — | WIBR3_shCTRL_TGFBi_rep1.fastq.gz | RNA-Seq | 1.7 GB | link | |||
| — | WIBR3_shCTRL_TGFBi_rep2.fastq.gz | RNA-Seq | 1.4 GB | link | |||
| — | WIBR3_shDDX6_TGFBi_rep1.fastq.gz | RNA-Seq | 1.6 GB | link | |||
| — | WIBR3_shDDX6_TGFBi_rep2.fastq.gz | RNA-Seq | 1.4 GB | link |