GSE112782
GSE GEOThe RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]
Organism:
Homo sapiens
Platform:
GPL20301
Samples:
10
Experiment Types:
Expression profiling by high throughput sequencing
Other
Submitted:
Apr 05 2018
Last Updated:
Oct 20 2019
Status:
Public on Oct 16 2019
Contact:
En-Ching,,Luo (UCSD)
Relations
SubSeries of: GSE112479
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA448944
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP137771
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
CLIP-seq
Analysis (5 steps)
View Data Processing
Processing steps for GSE112782
- Reads were adapter-trimmed and mapped to human-specific repetitive elements from RepBase (version 18.04) by STAR.
- Repeat-mapping reads were removed and remaining reads mapped to the human genome assembly hg19 with STAR.
- PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5â adapter and remaining reads retained as âusable readsâ.
- Peaks were called on the usable reads by CLIPper ,and assigned to gene regions annotated in Gencode (v19)
- Each peak was normalized to the size-matched input (SMInput)
Supplementary Files (1)
GSE112782_RAW.tar
Download
GEO Samples (10)
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 | |
|---|---|---|---|---|---|---|---|
| — | EY_INPUT_DCP1B_H1_S2_L006_R1_001.fastq.gz | RIP-Seq | 673.2 MB | link | |||
| — | EY_INPUT_FUS_H1_S1_L006_R1_001.fastq.gz | RIP-Seq | 477.5 MB | link | |||
| — | EY_INPUT_ILF2_H1_S3_L006_R1_001.fastq.gz | RIP-Seq | 618.7 MB | link | |||
| — | EY_IP_DCP1B_H1_S5_L006_R1_001.fastq.gz | RIP-Seq | 588.3 MB | link | |||
| — | EY_IP_FUS_H1_S4_L006_R1_001.fastq.gz | RIP-Seq | 567.4 MB | link | |||
| — | EY_IP_ILF2_H1_S6_L006_R1_001.fastq.gz | RIP-Seq | 455.5 MB | link | |||
| — | SA_DX6Ai_S97_L007_R1_001.fastq.gz | RIP-Seq | 2.1 GB | link | |||
| — | SA_DX6A_S98_L007_R1_001.fastq.gz | RIP-Seq | 1.6 GB | link | |||
| — | SA_DX6Bi_S99_L007_R1_001.fastq.gz | RIP-Seq | 1.7 GB | link | |||
| — | SA_DX6B_S100_L007_R1_001.fastq.gz | RIP-Seq | 900.5 MB | link |