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GSE125954

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

Organism: Homo sapiens
Platform: GPL18573
Samples: 6
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted: Jan 31 2019
Last Updated: Oct 16 2019
Status: Public on Oct 16 2019
Contact: Jocelyn,,Charlton (Harvard University)

Relations

SubSeries of: GSE112479 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA518086 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP183182

Summary

Analysis of adult and embryonic 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

ChIP-seq

Analysis (4 steps)

View Data Processing
Processing steps for GSE125954
  1. Reads were trimmed using cutadapt and aligned to the hg19 genome using BWA.
  2. Duplicate reads were marked using picard tools, and reads were filtered for a mapq score > 15.
  3. Macs2 callpeak was used to call peaks, with --broad used for H3K9me3.
  4. To generate peak sets, macs2 called peaks were extended by 500bp then only kept if present and overlapping in both biological replicates.

Supplementary Files (1)

GSE125954_RAW.tar Download
GEO Samples (6)
GSM3585963 GSM3585964 GSM3585965 GSM3585966 GSM3585967 GSM3585968

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 (6) and Runs (12)

Total: 1917 MB
SRX5315582 SRP183182 ChIP-Seq SINGLE
GSM3585963: GEN1C_sgCTRL_H3K4me3; Homo sapiens; ChIP-Seq
Sample: SRS4319212
BioProject: PRJNA518086
BioSample: SAMN10852577
Platform: ILLUMINA
Instrument: NextSeq 500
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 (2)
Run Spots Bases Size (MB) Files Link
SRR8511935 4513246 338493450 99.12 CTRL_H3K4me3_rep1.bam, SRR8511935, SRR8511935.sralite SRA
SRR8511936 9499499 702532798 172.58 CTRL_H3K4me3_rep2.bam, SRR8511936, SRR8511936.sralite SRA
SRX5315583 SRP183182 ChIP-Seq SINGLE
GSM3585964: GEN1C_sgCTRL_H3K27ac; Homo sapiens; ChIP-Seq
Sample: SRS4319211
BioProject: PRJNA518086
BioSample: SAMN10852619
Platform: ILLUMINA
Instrument: NextSeq 500
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 (2)
Run Spots Bases Size (MB) Files Link
SRR8511937 7666334 574975050 162.85 CTRL_H3K27ac_rep1.bam, SRR8511937, SRR8511937.sralite SRA
SRR8511938 9708068 715204594 177.16 CTRL_H3K27ac_rep2.bam, SRR8511938, SRR8511938.sralite SRA
SRX5315584 SRP183182 ChIP-Seq SINGLE
GSM3585965: GEN1C_sgCTRL_H3K9me3; Homo sapiens; ChIP-Seq
Sample: SRS4319213
BioProject: PRJNA518086
BioSample: SAMN10852618
Platform: ILLUMINA
Instrument: NextSeq 500
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 (2)
Run Spots Bases Size (MB) Files Link
SRR8511939 4811126 355487595 92.02 CTRL_H3K9me3_rep1.bam, SRR8511939, SRR8511939.sralite SRA
SRR8511940 16346151 1213944194 257.69 CTRL_H3K9me3_rep2.bam, SRR8511940, SRR8511940.sralite SRA
SRX5315585 SRP183182 ChIP-Seq SINGLE
GSM3585966: GEN1C_sgDDX6_H3K4me3; Homo sapiens; ChIP-Seq
Sample: SRS4319214
BioProject: PRJNA518086
BioSample: SAMN10852617
Platform: ILLUMINA
Instrument: NextSeq 500
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 (2)
Run Spots Bases Size (MB) Files Link
SRR8511941 5236428 392732100 113.21 DDX6_H3K4me3_rep1.bam, SRR8511941, SRR8511941.sralite SRA
SRR8511942 8333787 617496453 150.56 DDX6_H3K4me3_rep2.bam, SRR8511942, SRR8511942.sralite SRA
SRX5315586 SRP183182 ChIP-Seq SINGLE
GSM3585967: GEN1C_sgDDX6_H3K27ac; Homo sapiens; ChIP-Seq
Sample: SRS4319216
BioProject: PRJNA518086
BioSample: SAMN10852616
Platform: ILLUMINA
Instrument: NextSeq 500
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 (2)
Run Spots Bases Size (MB) Files Link
SRR8511943 6531824 489886800 136.43 DDX6_H3K27ac_rep1.bam, SRR8511943, SRR8511943.sralite SRA
SRR8511944 13042761 967477593 223.01 DDX6_H3K27ac_rep2.bam, SRR8511944, SRR8511944.sralite SRA
SRX5315587 SRP183182 ChIP-Seq SINGLE
GSM3585968: GEN1C_sgDDX6_H3K9me3; Homo sapiens; ChIP-Seq
Sample: SRS4319217
BioProject: PRJNA518086
BioSample: SAMN10852615
Platform: ILLUMINA
Instrument: NextSeq 500
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 (2)
Run Spots Bases Size (MB) Files Link
SRR8511945 4440626 327155123 87.45 DDX6_H3K9me3_rep1.bam, SRR8511945, SRR8511945.sralite SRA
SRR8511946 15443609 1146027677 244.51 DDX6_H3K9me3_rep2.bam, SRR8511946, SRR8511946.sralite SRA

Linked Publications (1)

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

Data Files (27)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— CTRL_H3K27ac_rep1.bam ChIP-Seq 162.8 MB link
— CTRL_H3K27ac_rep2.bam ChIP-Seq 177.2 MB link
— CTRL_H3K4me3_rep1.bam ChIP-Seq 99.1 MB link
— CTRL_H3K4me3_rep2.bam ChIP-Seq 172.6 MB link
— CTRL_H3K9me3_rep1.bam ChIP-Seq 92.0 MB link
— CTRL_H3K9me3_rep2.bam ChIP-Seq 257.7 MB link
— DDX6_H3K27ac_rep1.bam ChIP-Seq 136.4 MB link
— DDX6_H3K27ac_rep2.bam ChIP-Seq 223.0 MB link
— DDX6_H3K4me3_rep1.bam ChIP-Seq 113.2 MB link
— DDX6_H3K4me3_rep2.bam ChIP-Seq 150.6 MB link
— DDX6_H3K9me3_rep1.bam ChIP-Seq 87.4 MB link
— DDX6_H3K9me3_rep2.bam ChIP-Seq 244.5 MB link
— SRR8511935 ChIP-Seq 99.1 MB link
— SRR8511935_GSM3585963 ChIP-Seq 99.0 MB link
— SRR8511936_GSM3585963 ChIP-Seq 172.0 MB link
— SRR8511937_GSM3585964 ChIP-Seq 162.0 MB link
— SRR8511938 ChIP-Seq 177.2 MB link
— SRR8511938_GSM3585964 ChIP-Seq 177.0 MB link
— SRR8511939_GSM3585965 ChIP-Seq 92.0 MB link
— SRR8511940 ChIP-Seq 257.7 MB link
— SRR8511940_GSM3585965 ChIP-Seq 257.0 MB link
— SRR8511941_GSM3585966 ChIP-Seq 113.0 MB link
— SRR8511942_GSM3585966 ChIP-Seq 150.0 MB link
— SRR8511943_GSM3585967 ChIP-Seq 136.0 MB link
— SRR8511944_GSM3585967 ChIP-Seq 223.0 MB link
— SRR8511945_GSM3585968 ChIP-Seq 87.0 MB link
— SRR8511946_GSM3585968 ChIP-Seq 244.0 MB link