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Sample GSM2345052 Query DataSets for GSM2345052
Status Public on Jul 13, 2017
Title MV4;11_DMSO_RNA-seq Rep 3
Sample type SRA
Source name MV4;11_DMSO
Organism Homo sapiens
Characteristics cell line: MV4;11
tissue source: peripheral blood
cell type: macrophage
treated with: DMSO
Treatment protocol Cell lines were grown in 0.1% DMSO, 500nM JQ1 or 500nM JQ1–PA
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 3
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 fold‐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 Oct 14, 2016
Last update date May 15, 2019
Contact name Mark Dawson
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 (2)
GSE88750 Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [RNA-seq]
GSE88751 Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies
BioSample SAMN05908475
SRA SRX2245537

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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