GSE125809
GSE GEOThe RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]
Organism:
Homo sapiens
Platform:
GPL20301
Samples:
4
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Jan 29 2019
Last Updated:
Oct 16 2019
Status:
Public on Oct 16 2019
Contact:
En-Ching,,Luo (UCSD)
Relations
SubSeries of: GSE112479
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517602
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP182784
Summary
Analysis of DDX6 eCLIP in human skeletal myoblasts to identify DDX6 target genes, and binding locations.
Overall Design
Enhanced crosslinking and immunoprecipitation (eCLIP) was performed on Human Skeletal Myoblast cells
Analysis (6 steps)
View Data Processing
Processing steps for GSE125809
- library strategy: CLIP-seq
- 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)
GSE125809_RAW.tar
Download
GEO Samples (4)
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
SRA Experiments (4) and Runs (4)
Total: 2383 MBGSM3582123: Myo-DDX6-1-Input; Homo sapiens; RIP-Seq
Sample: SRS4303006
BioProject: PRJNA517602
BioSample: SAMN10839033
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Human Skeletal Myoblasts_input
cell type: Skeletal Muscle Cells
Original files (1)
Human Skeletal Myoblasts_input
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8501416 | 15315343 | 1148650725 | 422.68 | SRR8501416, SRR8501416.sralite | SRA |
GSM3582124: Myo-DDX6-2-Input; Homo sapiens; RIP-Seq
Sample: SRS4303007
BioProject: PRJNA517602
BioSample: SAMN10839032
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Human Skeletal Myoblasts_input
cell type: Skeletal Muscle Cells
Original files (1)
Human Skeletal Myoblasts_input
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8501417 | 19157847 | 1436838525 | 532.81 | SRR8501417, SRR8501417.sralite | SRA |
GSM3582125: Myo-DDX6-1-IP; Homo sapiens; RIP-Seq
Sample: SRS4303008
BioProject: PRJNA517602
BioSample: SAMN10839031
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Human Skeletal Myoblasts_DDX6 IP
cell type: Skeletal Muscle Cells
clip-seq antibody: DDX6 antibody; Genetex; GTX102795
Original files (1)
Human Skeletal Myoblasts_DDX6 IP
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8501418 | 26063883 | 1954791225 | 727.02 | SRR8501418, SRR8501418.sralite | SRA |
GSM3582126: Myo-DDX6-2-IP; Homo sapiens; RIP-Seq
Sample: SRS4303009
BioProject: PRJNA517602
BioSample: SAMN10839030
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Human Skeletal Myoblasts_DDX6 IP
cell type: Skeletal Muscle Cells
clip-seq antibody: DDX6 antibody; Genetex; GTX102795
Original files (1)
Human Skeletal Myoblasts_DDX6 IP
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8501419 | 25078289 | 1880871675 | 700.6 | SRR8501419, SRR8501419.sralite | SRA |
Linked Publications (1)
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019