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GSE112782

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

Organism: Homo sapiens
Platform: GPL20301
Samples: 10
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Apr 05 2018
Last Updated: Oct 20 2019
Status: Public on Oct 16 2019
Contact: En-Ching,,Luo (UCSD)

Relations

SubSeries of: GSE112479 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA448944 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP137771

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

CLIP-seq

Analysis (5 steps)

View Data Processing
Processing steps for GSE112782
  1. Reads were adapter-trimmed and mapped to human-specific repetitive elements from RepBase (version 18.04) by STAR.
  2. Repeat-mapping reads were removed and remaining reads mapped to the human genome assembly hg19 with STAR.
  3. PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5’ adapter and remaining reads retained as ‘usable reads’.
  4. Peaks were called on the usable reads by CLIPper ,and assigned to gene regions annotated in Gencode (v19)
  5. Each peak was normalized to the size-matched input (SMInput)

Supplementary Files (1)

GSE112782_RAW.tar Download
GEO Samples (10)
GSM3083443 GSM3083444 GSM3083445 GSM3083446 GSM3083447 GSM3083448 GSM3083449 GSM3083450 GSM3083451 GSM3083452

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 (10) and Runs (10)

Total: 9806 MB
SRX3893969 SRP137771 RIP-Seq PAIRED
GSM3083443: GEN1C-eCLIP-DDX6-1-Input; Homo sapiens; RIP-Seq
Sample: SRS3131573
BioProject: PRJNA448944
BioSample: SAMN08873836
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
clip-seq antibody: none
cell line: GEN1C
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950636 53696073 5906568030 2140.28 SA_DX6Ai_S97_L007_R1_001.fastq.gz, SA_DX6Ai_S97_L007_R2_001.fastq.gz,… SRA
SRX3893970 SRP137771 RIP-Seq PAIRED
GSM3083444: GEN1C-eCLIP-DDX6-2-Input; Homo sapiens; RIP-Seq
Sample: SRS3131572
BioProject: PRJNA448944
BioSample: SAMN08873835
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
clip-seq antibody: none
cell line: GEN1C
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950637 43132863 4744614930 1761.72 SA_DX6Bi_S99_L007_R1_001.fastq.gz, SA_DX6Bi_S99_L007_R2_001.fastq.gz,… SRA
SRX3893971 SRP137771 RIP-Seq PAIRED
GSM3083445: GEN1C-eCLIP-DDX6-1-IP; Homo sapiens; RIP-Seq
Sample: SRS3131574
BioProject: PRJNA448944
BioSample: SAMN08873834
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
clip-seq antibody: Bethyl, #A300-460A
cell line: GEN1C
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950638 39909517 4390046870 1623.17 SA_DX6A_S98_L007_R1_001.fastq.gz, SA_DX6A_S98_L007_R2_001.fastq.gz, S… SRA
SRX3893972 SRP137771 RIP-Seq PAIRED
GSM3083446: GEN1C-eCLIP-DDX6-2-IP; Homo sapiens; RIP-Seq
Sample: SRS3131576
BioProject: PRJNA448944
BioSample: SAMN08873833
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human induced pluripotent stem cells
clip-seq antibody: Bethyl, #A300-460A
cell line: GEN1C
cell type: primed hiPSCs
Original files (1)
human induced pluripotent stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950639 21664795 2383127450 900.51 SA_DX6B_S100_L007_R1_001.fastq.gz, SA_DX6B_S100_L007_R2_001.fastq.gz,… SRA
SRX3893973 SRP137771 RIP-Seq SINGLE
GSM3083447: H1-eCLIP-ILF2-Input; Homo sapiens; RIP-Seq
Sample: SRS3131578
BioProject: PRJNA448944
BioSample: SAMN08873832
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
clip-seq antibody: none
cell line: H1
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950640 22852187 1713914025 618.7 EY_INPUT_ILF2_H1_S3_L006_R1_001.fastq.gz, SRR6950640, SRR6950640.sral… SRA
SRX3893974 SRP137771 RIP-Seq SINGLE
GSM3083448: H1-eCLIP-FUS-Input; Homo sapiens; RIP-Seq
Sample: SRS3131577
BioProject: PRJNA448944
BioSample: SAMN08873831
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
clip-seq antibody: none
cell line: H1
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950641 18275391 1370654325 477.53 EY_INPUT_FUS_H1_S1_L006_R1_001.fastq.gz, SRR6950641, SRR6950641.srali… SRA
SRX3893975 SRP137771 RIP-Seq SINGLE
GSM3083449: H1-eCLIP-DCP1B-Input; Homo sapiens; RIP-Seq
Sample: SRS3131575
BioProject: PRJNA448944
BioSample: SAMN08873830
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
clip-seq antibody: none
cell line: H1
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950642 25550221 1916266575 673.25 EY_INPUT_DCP1B_H1_S2_L006_R1_001.fastq.gz, SRR6950642, SRR6950642.sra… SRA
SRX3893976 SRP137771 RIP-Seq SINGLE
GSM3083450: H1-eCLIP-ILF2-IP; Homo sapiens; RIP-Seq
Sample: SRS3131580
BioProject: PRJNA448944
BioSample: SAMN08873829
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
clip-seq antibody: Bethyl, #A303-147A
cell line: H1
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950643 17661197 1324589775 455.55 EY_IP_ILF2_H1_S6_L006_R1_001.fastq.gz, SRR6950643, SRR6950643.sralite SRA
SRX3893977 SRP137771 RIP-Seq SINGLE
GSM3083451: H1-eCLIP-FUS-IP; Homo sapiens; RIP-Seq
Sample: SRS3131579
BioProject: PRJNA448944
BioSample: SAMN08873828
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
clip-seq antibody: Bethyl, #A300-294A
cell line: H1
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950644 21910537 1643290275 567.39 EY_IP_FUS_H1_S4_L006_R1_001.fastq.gz, SRR6950644, SRR6950644.sralite SRA
SRX3893978 SRP137771 RIP-Seq SINGLE
GSM3083452: H1-eCLIP-DCP1B-IP; Homo sapiens; RIP-Seq
Sample: SRS3131581
BioProject: PRJNA448944
BioSample: SAMN08873827
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: human embryonic stem cells
clip-seq antibody: MBL, #RN112PW
cell line: H1
cell type: primed hESCs
Original files (1)
human embryonic stem cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6950645 22458528 1684389600 588.3 EY_IP_DCP1B_H1_S5_L006_R1_001.fastq.gz, SRR6950645, SRR6950645.sralite SRA

Linked Publications (1)

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

Data Files (12)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— EY_INPUT_DCP1B_H1_S2_L006_R1_001.fastq.gz RIP-Seq 673.2 MB link
— EY_INPUT_FUS_H1_S1_L006_R1_001.fastq.gz RIP-Seq 477.5 MB link
— EY_INPUT_ILF2_H1_S3_L006_R1_001.fastq.gz RIP-Seq 618.7 MB link
— EY_IP_DCP1B_H1_S5_L006_R1_001.fastq.gz RIP-Seq 588.3 MB link
— EY_IP_FUS_H1_S4_L006_R1_001.fastq.gz RIP-Seq 567.4 MB link
— EY_IP_ILF2_H1_S6_L006_R1_001.fastq.gz RIP-Seq 455.5 MB link
— SA_DX6Ai_S97_L007_R1_001.fastq.gz RIP-Seq 2.1 GB link
— SA_DX6A_S98_L007_R1_001.fastq.gz RIP-Seq 1.6 GB link
— SA_DX6Bi_S99_L007_R1_001.fastq.gz RIP-Seq 1.7 GB link
— SA_DX6B_S100_L007_R1_001.fastq.gz RIP-Seq 900.5 MB link
— SRR6950639 RIP-Seq 900.5 MB link
— SRR6950641 RIP-Seq 477.5 MB link