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Sample GSM2143668 Query DataSets for GSM2143668
Status Public on Jun 20, 2016
Title DMSO shBRD4 Rep 2
Sample type SRA
 
Source name MV4;11 cell line
Organism Homo sapiens
Characteristics tissue: peripheral blood
cell line: MV4;11
cell type: macrophage
Treatment protocol Cell lines were transduced with a BRD4 or scramble shRNA with DMSO or 5uM of SGC0946
Growth protocol Cell lines were grown in RPMI-1640 supplemented with 20% fetal calf serum, penicillin (100 units/mL) and streptomycin (100 ug/mL)
Extracted molecule polyA RNA
Extraction protocol RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Replicate 2
Data processing Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a foldā€change greater than 2 were considered significantly differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalised expression values for all Samples
 
Submission date May 05, 2016
Last update date May 15, 2019
Contact name Mark Dawson
E-mail(s) mark.dawson@petermac.org
Organization name Peter MacCallum Cancer Centre
Street address 305 Grattan Street
City Melbourne
State/province VIC
ZIP/Postal code 3000
Country Australia
 
Platform ID GPL11154
Series (1)
GSE81148 RNASeq of MV4;11 cells transduced with scramble shRNA or BRD4 shRNA in combination with DMSO or SGC0946
Relations
BioSample SAMN04956449
SRA SRX1743624

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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