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GSE125808

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

Organism: Homo sapiens
Platform: GPL20301
Samples: 36
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/PRJNA517601 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP182783

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

Polysome cells were treated with cycloheximide (CHX) at 100 µg/ml for 5 min at 37°C. And then resuspend in polysome lysis buffer, loaded on the sucrose gradient and centrifuged at 35,000 x g (Beckman, rotor SW41) at 4 °C for 3 h. 500 µl fraction were collected using a FC203B (Gilson) fraction collector. Fractions containing monosome(MONO), light polysome (LITE), medium polysome (MID), heavy polysome (HEAVY), and total polsome (POLY) were pooled.

Analysis (4 steps)

View Data Processing
Processing steps for GSE125808
  1. RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i).
  2. Reads did not map to repetitive elements were then mapped to the human genome (hg19).
  3. Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
  4. The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.

Supplementary Files (2)

GSE125808_control_RPKM.csv.gz Download
GSE125808_sgRNA_RPKM.csv.gz Download
GEO Samples (36)
GSM3582087 GSM3582088 GSM3582089 GSM3582090 GSM3582091 GSM3582092 GSM3582093 GSM3582094 GSM3582095 GSM3582096 GSM3582097 GSM3582098 GSM3582099 GSM3582100 GSM3582101 GSM3582102 GSM3582103 GSM3582104 GSM3582105 GSM3582106 GSM3582107 GSM3582108 GSM3582109 GSM3582110 GSM3582111 GSM3582112 GSM3582113 GSM3582114 GSM3582115 GSM3582116 GSM3582117 GSM3582118 GSM3582119 GSM3582120 GSM3582121 GSM3582122

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

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
— SRR8501406 RNA-Seq 602.5 MB link
— SRR8501407 RNA-Seq 590.9 MB link
— SRR8501408 RNA-Seq 429.8 MB link
— SRR8501409 RNA-Seq 606.9 MB link
— SRR8501410 RNA-Seq 359.6 MB link
— SRR8501411 RNA-Seq 716.7 MB link
— SRR8501412 RNA-Seq 621.7 MB link
— SRR8501413 RNA-Seq 654.2 MB link
— SRR8501414 RNA-Seq 754.0 MB link
— SRR8501415 RNA-Seq 529.2 MB link