← All datasets

GSE124072

GSE GEO
View on GEO Export SRA CSV

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-Seq]

Organism: Homo sapiens
Platform: GPL11154
Samples: 8
Experiment Types:
Expression 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/PRJNA510653 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP173835

Summary

Analysis of adult progenitor 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

RNA-seq

Analysis (3 steps)

View Data Processing
Processing steps for GSE124072
  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 STAR
  3. Transcript abundance was calculated using Htseq

Supplementary Files (1)

GSE124072_RAW.tar Download
GEO Samples (8)
GSM3520094 GSM3520095 GSM3520096 GSM3520097 GSM3520098 GSM3520099 GSM3520100 GSM3520101

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: 12897 MB
SRX5162002 SRP173835 RNA-Seq PAIRED
GSM3520094: NPC shCTRL rep1; Homo sapiens; RNA-Seq
Sample: SRS4171250
BioProject: PRJNA510653
BioSample: SAMN10612673
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human neural progenitor cells
treatment: shCTRL
cell type: neural progenitor cells
Original files (1)
human neural progenitor cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351040 29378588 2996615976 1751.33 NPC.shCTRL_1.R1.fastq.gz, NPC.shCTRL_1.R2.fastq.gz, SRR8351040, SRR83… SRA
SRX5162003 SRP173835 RNA-Seq PAIRED
GSM3520095: NPC shCTRL rep2; Homo sapiens; RNA-Seq
Sample: SRS4171252
BioProject: PRJNA510653
BioSample: SAMN10612672
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human neural progenitor cells
treatment: shCTRL
cell type: neural progenitor cells
Original files (1)
human neural progenitor cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351041 16601029 1693304958 996.94 NPC.shCTRL_2.R1.fastq.gz, NPC.shCTRL_2.R2.fastq.gz, SRR8351041, SRR83… SRA
SRX5162004 SRP173835 RNA-Seq PAIRED
GSM3520096: NPC shDDX6 rep1; Homo sapiens; RNA-Seq
Sample: SRS4171251
BioProject: PRJNA510653
BioSample: SAMN10612671
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human neural progenitor cells
treatment: shDDX6
cell type: neural progenitor cells
Original files (1)
human neural progenitor cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351042 26871612 2740904424 1603.9 NPC.shDDX6_1.R1.fastq.gz, NPC.shDDX6_1.R2.fastq.gz, SRR8351042, SRR83… SRA
SRX5162005 SRP173835 RNA-Seq PAIRED
GSM3520097: NPC shDDX6 rep2; Homo sapiens; RNA-Seq
Sample: SRS4171253
BioProject: PRJNA510653
BioSample: SAMN10612670
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human neural progenitor cells
treatment: shDDX6
cell type: neural progenitor cells
Original files (1)
human neural progenitor cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351043 37782173 3853781646 2263.81 NPC.shDDX6_2.R1.fastq.gz, NPC.shDDX6_2.R2.fastq.gz, SRR8351043, SRR83… SRA
SRX5162006 SRP173835 RNA-Seq PAIRED
GSM3520098: Myoblast shCTRL rep1; Homo sapiens; RNA-Seq
Sample: SRS4171254
BioProject: PRJNA510653
BioSample: SAMN10612669
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: shCTRL
cell type: myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351044 22522390 2297283780 1353.19 Myoblast.shCTRL_1.R1.fastq.gz, Myoblast.shCTRL_1.R2.fastq.gz, SRR8351… SRA
SRX5162007 SRP173835 RNA-Seq PAIRED
GSM3520099: Myoblast shCTRL rep2; Homo sapiens; RNA-Seq
Sample: SRS4171255
BioProject: PRJNA510653
BioSample: SAMN10612668
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: shCTRL
cell type: myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351045 29158300 2974146600 1739.47 Myoblast.shCTRL_2.R1.fastq.gz, Myoblast.shCTRL_2.R2.fastq.gz, SRR8351… SRA
SRX5162008 SRP173835 RNA-Seq PAIRED
GSM3520100: Myoblast shDDX6 rep1; Homo sapiens; RNA-Seq
Sample: SRS4171256
BioProject: PRJNA510653
BioSample: SAMN10612667
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: shDDX6
cell type: myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351046 25542950 2605380900 1533.12 Myoblast.shDDX6_1.R1.fastq.gz, Myoblast.shDDX6_1.R2.fastq.gz, SRR8351… SRA
SRX5162009 SRP173835 RNA-Seq PAIRED
GSM3520101: Myoblast shDDX6 rep2; Homo sapiens; RNA-Seq
Sample: SRS4171257
BioProject: PRJNA510653
BioSample: SAMN10612666
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human myoblasts
treatment: shDDX6
cell type: myoblasts
Original files (1)
human myoblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8351047 27490879 2804069658 1655.62 Myoblast.shDDX6_2.R1.fastq.gz, Myoblast.shDDX6_2.R2.fastq.gz, SRR8351… 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
— Myoblast.shCTRL_1.R1.fastq.gz RNA-Seq 1.3 GB link
— Myoblast.shCTRL_2.R1.fastq.gz RNA-Seq 1.7 GB link
— Myoblast.shDDX6_1.R1.fastq.gz RNA-Seq 1.5 GB link
— Myoblast.shDDX6_2.R1.fastq.gz RNA-Seq 1.6 GB link
— Myoblast.shDDX6_2.R2.fastq.gz RNA-Seq 1.6 GB link
— NPC.shCTRL_1.R1.fastq.gz RNA-Seq 1.7 GB link
— NPC.shCTRL_2.R1.fastq.gz RNA-Seq 996.9 MB link
— NPC.shDDX6_1.R1.fastq.gz RNA-Seq 1.6 GB link
— NPC.shDDX6_2.R1.fastq.gz RNA-Seq 2.2 GB link
— SRR8351040 RNA-Seq 1.7 GB link