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Sample GSM1395372 Query DataSets for GSM1395372
Status Public on Jun 30, 2016
Title mock_DMSO_8hr rep2
Sample type SRA
 
Source name colorectal carcinoma cell line
Organism Homo sapiens
Characteristics cell line: vorinostat-resistant HCT116
treatment: mock DMSO
timepoint: 8hr
Treatment protocol Cells were reverse transfected in 12 well plates with the appropriate siRNA (final concentration 40nM, Dharmacon siGENOME SMARTpools, Thermo Fisher) or lipid only as a control (mock transfection). Each well contained 3.5 x 10^5 cells and 1.0ul of Dharmafect 2 (Thermo Fisher). Media was refreshed after 24hrs and after 48hrs, cells were treated with 2.5uM vorinostat or DMSO (solvent) as a control. Cells were harvested by trypsinisation after 4hrs, 8hrs or 12hrs of drug treatment.
Growth protocol Cells were cultured in RPMI 1640 (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% sodium pyruvate, 2.5g/L glucose.
Extracted molecule total RNA
Extraction protocol RNA was extracted from cells using the Rneasy RNA extraction kit (QIAGEN) as per the manufacturer's protocol. RNA was quantitated using spectrophotometry (Nanodrop).
2ug RNA was prepared for sequencing using the TruSeq RNA Sample Preparation v2 Guide with all kit reagents purchased from Illumina.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description KF-3
Data processing Illumina Casava 1.8.2 software used for basecalling.
Reads were quality checked by FastQC and trimmed if necessary for low base quality or adaptor, and then mapped to the human reference genome (GRCh37) using Tophat2 v.2.0.8b with maximum number of multiple hits set to 1 and using the option to map first to the reference transcriptome (Ensembl v69).
Counts per gene were obtained using HTSeq and normalised using the limma-voom method.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample
 
Submission date May 21, 2014
Last update date May 15, 2019
Contact name Katrina Joy Falkenberg
E-mail(s) katrina.falkenberg@imp.ac.at
Organization name Peter MacCallum Cancer Centre
Department Research Division
Lab Gene Regulation Laboratory
Street address St Andrews Place
City East Melbourne
State/province Victoria
ZIP/Postal code 3002
Country Australia
 
Platform ID GPL16791
Series (1)
GSE57871 RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of GLI1 or PSMD13 with or without vorinostat treatment
Relations
BioSample SAMN02796592
SRA SRX548964

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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