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GSE112383

GSE GEO
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The 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
  1. STAR was used to map sequencing reads to human reference genome (Ensembl annotation of hg19 assembly).
  2. Read counts over transcripts were calculated using HTSeq v.0.6.0 based on Ensembl annotation of hg19 genome.
  3. Differential expression analysis was performed using EdgeR.

Supplementary Files (3)

GSE112383_Samples_DDX_TEs_complete_RPKM_table.txt.gz Download
GSE112383_Samples_naive_complete_RPKM_table.txt.gz Download
GSE112383_Samples_sgDDX6_complete_RPKM_table.txt.gz Download
GEO Samples (18)
GSM3069316 GSM3069317 GSM3069318 GSM3069319 GSM3069320 GSM3069321 GSM3069322 GSM3069323 GSM3069324 GSM3069325 GSM3069326 GSM3069327 GSM3069328 GSM3069329 GSM3069330 GSM3069331 GSM3069332 GSM3069333

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 (18) and Runs (18)

Total: 26391 MB
SRX3852714 SRP136549 RNA-Seq SINGLE
GSM3069316: WIBR3 shCTRL rep1; Homo sapiens; RNA-Seq
Sample: SRS3096888
BioProject: PRJNA445858
BioSample: SAMN08800956
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903969 37716524 1923542724 1321.03 WIBR3_shCTRL_rep1.fastq.gz, SRR6903969, SRR6903969.sralite SRA
SRX3852715 SRP136549 RNA-Seq SINGLE
GSM3069317: WIBR3 shCTRL rep2; Homo sapiens; RNA-Seq
Sample: SRS3096887
BioProject: PRJNA445858
BioSample: SAMN08800955
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903970 43002316 2193118116 1494.01 WIBR3_shCTRL_rep2.fastq.gz, SRR6903970, SRR6903970.sralite SRA
SRX3852716 SRP136549 RNA-Seq SINGLE
GSM3069318: WIBR3 shDDX6 rep1; Homo sapiens; RNA-Seq
Sample: SRS3096889
BioProject: PRJNA445858
BioSample: SAMN08800985
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903971 43286398 2207606298 1513.67 WIBR3_shDDX6_rep1.fastq.gz, SRR6903971, SRR6903971.sralite SRA
SRX3852717 SRP136549 RNA-Seq SINGLE
GSM3069319: WIBR3 shDDX6 rep2; Homo sapiens; RNA-Seq
Sample: SRS3096890
BioProject: PRJNA445858
BioSample: SAMN08800984
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903972 40735890 2077530390 1419.4 WIBR3_shDDX6_rep2.fastq.gz, SRR6903972, SRR6903972.sralite SRA
SRX3852718 SRP136549 RNA-Seq SINGLE
GSM3069320: GEN1C sgCTRL rep1; Homo sapiens; RNA-Seq
Sample: SRS3096891
BioProject: PRJNA445858
BioSample: SAMN08800983
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903974 41973986 2140673286 1460.84 GEN1C_sgCTRL_rep1.fastq.gz, SRR6903974, SRR6903974.sralite SRA
SRX3852719 SRP136549 RNA-Seq SINGLE
GSM3069321: GEN1C sgCTRL rep2; Homo sapiens; RNA-Seq
Sample: SRS3096892
BioProject: PRJNA445858
BioSample: SAMN08800982
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903976 64291544 3278868744 2253.3 GEN1C_sgCTRL_rep2.fastq.gz, SRR6903976, SRR6903976.sralite SRA
SRX3852720 SRP136549 RNA-Seq SINGLE
GSM3069322: GEN1C sgDDX6 rep1; Homo sapiens; RNA-Seq
Sample: SRS3096893
BioProject: PRJNA445858
BioSample: SAMN08800981
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903977 48160698 2456195598 1672.04 GEN1C_sgDDX6_rep1.fastq.gz, SRR6903977, SRR6903977.sralite SRA
SRX3852721 SRP136549 RNA-Seq SINGLE
GSM3069323: GEN1C sgDDX6 rep2; Homo sapiens; RNA-Seq
Sample: SRS3096894
BioProject: PRJNA445858
BioSample: SAMN08800980
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903978 41453954 2114151654 1441.06 GEN1C_sgDDX6_rep2.fastq.gz, SRR6903978, SRR6903978.sralite SRA
SRX3852722 SRP136549 RNA-Seq SINGLE
GSM3069324: WIBR3 shCTRL TGFBi rep1; Homo sapiens; RNA-Seq
Sample: SRS3096895
BioProject: PRJNA445858
BioSample: SAMN08800979
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903979 50060067 2553063417 1752.88 WIBR3_shCTRL_TGFBi_rep1.fastq.gz, SRR6903979, SRR6903979.sralite SRA
SRX3852723 SRP136549 RNA-Seq SINGLE
GSM3069325: WIBR3 shCTRL TGFBi rep2; Homo sapiens; RNA-Seq
Sample: SRS3096896
BioProject: PRJNA445858
BioSample: SAMN08800908
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903980 41612018 2122212918 1449.59 WIBR3_shCTRL_TGFBi_rep2.fastq.gz, SRR6903980, SRR6903980.sralite SRA
SRX3852724 SRP136549 RNA-Seq SINGLE
GSM3069326: WIBR3 shDDX6 TGFBi rep1; Homo sapiens; RNA-Seq
Sample: SRS3096897
BioProject: PRJNA445858
BioSample: SAMN08800907
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903981 47158070 2405061570 1650.74 WIBR3_shDDX6_TGFBi_rep1.fastq.gz, SRR6903981, SRR6903981.sralite SRA
SRX3852725 SRP136549 RNA-Seq SINGLE
GSM3069327: WIBR3 shDDX6 TGFBi rep2; Homo sapiens; RNA-Seq
Sample: SRS3096898
BioProject: PRJNA445858
BioSample: SAMN08800978
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903982 39997078 2039850978 1397.42 WIBR3_shDDX6_TGFBi_rep2.fastq.gz, SRR6903982, SRR6903982.sralite SRA
SRX3852726 SRP136549 RNA-Seq SINGLE
GSM3069328: GEN1C sgCTRL TGFBi rep1; Homo sapiens; RNA-Seq
Sample: SRS3096899
BioProject: PRJNA445858
BioSample: SAMN08800977
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903983 45073828 2298765228 1566.62 GEN1C_sgCTRL_TGFBi_rep1.fastq.gz, SRR6903983, SRR6903983.sralite SRA
SRX3852727 SRP136549 RNA-Seq SINGLE
GSM3069329: GEN1C sgCTRL TGFBi rep2; Homo sapiens; RNA-Seq
Sample: SRS3096901
BioProject: PRJNA445858
BioSample: SAMN08800957
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903984 42293087 2156947437 1470.93 GEN1C_sgCTRL_TGFBi_rep2.fastq.gz, SRR6903984, SRR6903984.sralite SRA
SRX3852728 SRP136549 RNA-Seq SINGLE
GSM3069330: GEN1C sgDDX6 TGFBi rep1; Homo sapiens; RNA-Seq
Sample: SRS3096900
BioProject: PRJNA445858
BioSample: SAMN08800883
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903985 40844925 2083091175 1421.92 GEN1C_sgDDX6_TGFBi_rep1.fastq.gz, SRR6903985, SRR6903985.sralite SRA
SRX3852729 SRP136549 RNA-Seq SINGLE
GSM3069331: GEN1C sgDDX6 TGFBi rep2; Homo sapiens; RNA-Seq
Sample: SRS3096903
BioProject: PRJNA445858
BioSample: SAMN08800882
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903986 39978137 2038884987 1387.48 GEN1C_sgDDX6_TGFBi_rep2.fastq.gz, SRR6903986, SRR6903986.sralite SRA
SRX3852730 SRP136549 RNA-Seq SINGLE
GSM3069332: WIBR3 Naïve rep1; Homo sapiens; RNA-Seq
Sample: SRS3096902
BioProject: PRJNA445858
BioSample: SAMN08800881
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: naive hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903987 23835203 1215595353 894.96 WIBR3_Naive_rep1.fastq.gz, SRR6903987, SRR6903987.sralite SRA
SRX3852731 SRP136549 RNA-Seq SINGLE
GSM3069333: WIBR3 Naïve rep2; Homo sapiens; RNA-Seq
Sample: SRS3096904
BioProject: PRJNA445858
BioSample: SAMN08800880
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
cell type: naive hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6903988 21836185 1113645435 823.3 WIBR3_Naive_rep2.fastq.gz, SRR6903988, SRR6903988.sralite SRA

Linked Publications (1)

The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019

Data Files (18)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— GEN1C_sgCTRL_rep1.fastq.gz RNA-Seq 1.4 GB link
— GEN1C_sgCTRL_rep2.fastq.gz RNA-Seq 2.2 GB link
— 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_rep1.fastq.gz RNA-Seq 1.6 GB link
— GEN1C_sgDDX6_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_rep1.fastq.gz RNA-Seq 1.3 GB link
— WIBR3_shCTRL_rep2.fastq.gz RNA-Seq 1.5 GB 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_rep1.fastq.gz RNA-Seq 1.5 GB link
— WIBR3_shDDX6_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