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GSE142307

GSE GEO
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Effect of Stau2 knockdown on H3K4 methylation in human bcCML cells (K562)

Organism: Homo sapiens
Platform: GPL16791
Samples: 6
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted: Dec 18 2019
Last Updated: Apr 23 2020
Status: Public on Apr 21 2020
Contact: Michael,,Hamilton (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA596503 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP238109

Summary

Evaluating the effect of Stau2 knockdown on H3K4me1, H3K4me2, H3K4me3 in K562 cells

Overall Design

ChIP-seq comparative analysis of shControl and shStau2 infected human K562 cells

Analysis (2 steps)

View Data Processing
Processing steps for GSE142307
  1. Bowtie2-alignment tool
  2. Macs2-peak calling

Supplementary Files (1)

GSE142307_RAW.tar Download
GEO Samples (6)
GSM4224976 GSM4224977 GSM4224979 GSM4224980 GSM4224981 GSM4224982

SRA Experiments (6) and Runs (6)

Total: 6973 MB
SRX7411418 SRP238109 ChIP-Seq SINGLE
GSM4224976: bcCML shControl H3K4me2; Homo sapiens; ChIP-Seq
Sample: SRS5858615
BioProject: PRJNA596503
BioSample: SAMN13625033
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
cell line: K562 cells
condition: Control shRNA
antibody: H3K4me2
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10735581 42989965 3267237340 1202.8 shCtrl_H3K4me2.fastq.gz, SRR10735581, SRR10735581.sralite SRA
SRX7411419 SRP238109 ChIP-Seq SINGLE
GSM4224977: bcCML shControl H3K4me3; Homo sapiens; ChIP-Seq
Sample: SRS5858617
BioProject: PRJNA596503
BioSample: SAMN13625032
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
cell line: K562 cells
condition: Control shRNA
antibody: H3K4me3
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10735582 49301029 3746878204 1369.32 shCtrl_H3K4me3.fastq.gz, SRR10735582, SRR10735582.sralite SRA
SRX7411421 SRP238109 ChIP-Seq SINGLE
GSM4224979: bcCML shStaufen 2 H3K4me2; Homo sapiens; ChIP-Seq
Sample: SRS5858619
BioProject: PRJNA596503
BioSample: SAMN13625029
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
cell line: K562 cells
condition: Stau2 shRNA
antibody: H3K4me2
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10735584 48111145 3656447020 1341.89 shStau2_H3K4me2.fastq.gz, SRR10735584, SRR10735584.sralite SRA
SRX7411422 SRP238109 ChIP-Seq SINGLE
GSM4224980: bcCML shStaufen 2 H3K4me3; Homo sapiens; ChIP-Seq
Sample: SRS5858620
BioProject: PRJNA596503
BioSample: SAMN13625027
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
cell line: K562 cells
condition: Stau2 shRNA
antibody: H3K4me3
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10735585 45348856 3446513056 1253.27 shStau2_H3K4me3.fastq.gz, SRR10735585, SRR10735585.sralite SRA
SRX7411423 SRP238109 ChIP-Seq SINGLE
GSM4224981: bcCML Control shRNA input; Homo sapiens; ChIP-Seq
Sample: SRS5858621
BioProject: PRJNA596503
BioSample: SAMN13625026
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
cell line: K562 cells
condition: Control shRNA
antibody: input
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10735586 31377720 2384706720 881.82 shCtrl_Input.fastq.gz, SRR10735586, SRR10735586.sralite SRA
SRX7411424 SRP238109 ChIP-Seq SINGLE
GSM4224982: bcCML shStaufen 2 shRNA input; Homo sapiens; ChIP-Seq
Sample: SRS5858622
BioProject: PRJNA596503
BioSample: SAMN13625025
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
cell line: K562 cells
condition: Stau2 shRNA
antibody: input
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10735587 32693277 2484689052 924.19 shStau2_Input.fastq.gz, SRR10735587, SRR10735587.sralite SRA

Linked Publications (1)

An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.
Nature cancer · 2020

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— shCtrl_H3K4me2.fastq.gz ChIP-Seq 1.2 GB link
— shCtrl_H3K4me3.fastq.gz ChIP-Seq 1.3 GB link
— shCtrl_Input.fastq.gz ChIP-Seq 881.8 MB link
— shStau2_H3K4me2.fastq.gz ChIP-Seq 1.3 GB link
— shStau2_H3K4me3.fastq.gz ChIP-Seq 1.2 GB link
— shStau2_Input.fastq.gz ChIP-Seq 924.2 MB link