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GSE124071

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The 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
  1. Illumina Casava1.7 software used for basecalling.
  2. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using BWA
  3. peaks were called using HOTSPOT with default parameter

Supplementary Files (1)

GSE124071_RAW.tar Download
GEO Samples (8)
GSM3520086 GSM3520087 GSM3520088 GSM3520089 GSM3520090 GSM3520091 GSM3520092 GSM3520093

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 (8) and Runs (8)

Total: 18406 MB
SRX5162010 SRP173836 ATAC-seq PAIRED
GSM3520086: GEN1C sgCTRL_rep1; Homo sapiens; ATAC-seq
Sample: SRS4171258
BioProject: PRJNA510652
BioSample: SAMN10612665
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
treatment: sgCTRL
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351048 45321598 4622802996 2562.52 iPSC.CTRL.1.R1.fastq.gz, iPSC.CTRL.1.R2.fastq.gz, SRR8351048, SRR8351… SRA
SRX5162011 SRP173836 ATAC-seq PAIRED
GSM3520087: GEN1C sgCTRL_rep2; Homo sapiens; ATAC-seq
Sample: SRS4171260
BioProject: PRJNA510652
BioSample: SAMN10612664
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
treatment: sgCTRL
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351049 42556755 4340789010 2410.52 iPSC.CTRL.2.R1.fastq.gz, iPSC.CTRL.2.R2.fastq.gz, SRR8351049, SRR8351… SRA
SRX5162012 SRP173836 ATAC-seq PAIRED
GSM3520088: GEN1C sgDDX6_rep1; Homo sapiens; ATAC-seq
Sample: SRS4171259
BioProject: PRJNA510652
BioSample: SAMN10612663
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
treatment: sgDDX6
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351050 39932144 4073078688 2255.39 iPSC.DDX6.1.R1.fastq.gz, iPSC.DDX6.1.R2.fastq.gz, SRR8351050, SRR8351… SRA
SRX5162013 SRP173836 ATAC-seq PAIRED
GSM3520089: GEN1C sgDDX6_rep2; Homo sapiens; ATAC-seq
Sample: SRS4171262
BioProject: PRJNA510652
BioSample: SAMN10612662
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
treatment: sgDDX6
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351051 42005738 4284585276 2360.9 iPSC.DDX6.2.R1.fastq.gz, iPSC.DDX6.2.R2.fastq.gz, SRR8351051, SRR8351… SRA
SRX5162014 SRP173836 ATAC-seq PAIRED
GSM3520090: Myoblast shCTRL_rep1; Homo sapiens; ATAC-seq
Sample: SRS4171261
BioProject: PRJNA510652
BioSample: SAMN10612661
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: sgCTRL
cell type: human myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351052 42194536 4303842672 2412.23 Myoblast.CTRL.1.R1.fastq.gz, Myoblast.CTRL.1.R2.fastq.gz, SRR8351052,… SRA
SRX5162015 SRP173836 ATAC-seq PAIRED
GSM3520091: Myoblast shCTRL_rep2; Homo sapiens; ATAC-seq
Sample: SRS4171264
BioProject: PRJNA510652
BioSample: SAMN10612660
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: sgCTRL
cell type: human myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351053 35989037 3670881774 2059.7 Myoblast.CTRL.2.R1.fastq.gz, Myoblast.CTRL.2.R2.fastq.gz, SRR8351053,… SRA
SRX5162016 SRP173836 ATAC-seq PAIRED
GSM3520092: Myoblast shDDX6_rep1; Homo sapiens; ATAC-seq
Sample: SRS4171263
BioProject: PRJNA510652
BioSample: SAMN10612659
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: sgDDX6
cell type: human myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351054 35777745 3649329990 1999.63 Myoblast.DDX6.1.R1.fastq.gz, Myoblast.DDX6.1.R2.fastq.gz, SRR8351054,… SRA
SRX5162017 SRP173836 ATAC-seq PAIRED
GSM3520093: Myoblast shDDX6_rep2; Homo sapiens; ATAC-seq
Sample: SRS4171265
BioProject: PRJNA510652
BioSample: SAMN10612658
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: sgDDX6
cell type: human myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351055 41975197 4281470094 2345.17 Myoblast.DDX6.2.R1.fastq.gz, Myoblast.DDX6.2.R2.fastq.gz, SRR8351055,… SRA

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
— 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.1.R2.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