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GSE135012

GSE GEO
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Stau2 knockdown in human bcCML cells (K562)"

Organism: Homo sapiens
Platform: GPL11154
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jul 29 2019
Last Updated: Apr 21 2020
Status: Public on Apr 21 2020
Contact: Michael,,Hamilton (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA557137 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP216662

Summary

STAU2 knockdown in human K562 cells

Overall Design

RNA-seq comparative analysis of shControl and shSTAU2 infected K562 cells

Analysis (2 steps)

View Data Processing
Processing steps for GSE135012
  1. Kallisto – transcript quantification
  2. Sleuth – gene differential expression analysis/gene normalized abundance measurements

Supplementary Files (2)

GSE135012_sleuth5.txt.gz Download
GSE135012_tpm_values.txt.gz Download
GEO Samples (6)
GSM3983624 GSM3983625 GSM3983626 GSM3983627 GSM3983628 GSM3983629

SRA Experiments (6) and Runs (6)

Total: 10790 MB
SRX6607843 SRP216662 RNA-Seq PAIRED
GSM3983624: bcCML Control shRNA Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS5172317
BioProject: PRJNA557137
BioSample: SAMN12390033
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
tissue: K562 cells
condition: Control shRNA
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9853389 25516718 5103343600 2008.18 CRT1_1.fastq.gz, CRT1_2.fastq.gz, SRR9853389, SRR9853389.sralite SRA
SRX6607844 SRP216662 RNA-Seq PAIRED
GSM3983625: bcCML Control shRNA Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS5172318
BioProject: PRJNA557137
BioSample: SAMN12390032
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
tissue: K562 cells
condition: Control shRNA
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9853390 25702983 5140596600 2022.39 CRT2_1.fastq.gz, CRT2_2.fastq.gz, SRR9853390, SRR9853390.sralite SRA
SRX6607845 SRP216662 RNA-Seq PAIRED
GSM3983626: bcCML Control shRNA Replicate 3; Homo sapiens; RNA-Seq
Sample: SRS5172319
BioProject: PRJNA557137
BioSample: SAMN12390031
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
tissue: K562 cells
condition: Control shRNA
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9853391 23864209 4772841800 1877.54 CRT3_1.fastq.gz, CRT3_2.fastq.gz, SRR9853391, SRR9853391.sralite SRA
SRX6607846 SRP216662 RNA-Seq PAIRED
GSM3983627: bcCML Stau2 shRNA Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS5172320
BioProject: PRJNA557137
BioSample: SAMN12390030
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
tissue: K562 cells
condition: STAU2 shRNA
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9853392 20415325 4083065000 1760.38 STAU1_1.fastq.gz, STAU1_2.fastq.gz, SRR9853392, SRR9853392.sralite SRA
SRX6607847 SRP216662 RNA-Seq PAIRED
GSM3983628: bcCML Stau2 shRNA Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS5172322
BioProject: PRJNA557137
BioSample: SAMN12390029
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
tissue: K562 cells
condition: STAU2 shRNA
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9853393 17536496 3507299200 1410.07 STAU2_1.fastq.gz, STAU2_2.fastq.gz, SRR9853393, SRR9853393.sralite SRA
SRX6607848 SRP216662 RNA-Seq PAIRED
GSM3983629: bcCML Stau2 shRNA Replicate 3; Homo sapiens; RNA-Seq
Sample: SRS5172321
BioProject: PRJNA557137
BioSample: SAMN12390028
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: K562 cells
tissue: K562 cells
condition: STAU2 shRNA
Original files (1)
K562 cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR9853394 19942245 3988449000 1711.73 STAU3_1.fastq.gz, STAU3_2.fastq.gz, SRR9853394, SRR9853394.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
— CRT1_1.fastq.gz RNA-Seq 2.0 GB link
— CRT2_1.fastq.gz RNA-Seq 2.0 GB link
— CRT3_1.fastq.gz RNA-Seq 1.8 GB link
— STAU1_1.fastq.gz RNA-Seq 1.7 GB link
— STAU2_1.fastq.gz RNA-Seq 1.4 GB link
— STAU3_1.fastq.gz RNA-Seq 1.7 GB link