Comment[ArrayExpressAccession]	E-GEOD-37640
MAGE-TAB Version	1.1				
Public Release Date	2013-04-22
Investigation Title	Gene expression profile of TARDBP in hepatocellular carcinoma cell line (SK-Hep1)				
Comment[Submitted Name]	Gene expression profile of TARDBP in hepatocellular carcinoma cell line (SK-Hep1)
Experiment Description	TARDBP is TARDBP (TDP-43) is a DNA/RNA binding protein and was mutated in human amyotrophic lateral sclerosis (ALS). However, its function in human cancer has not been fully identified, yet.Thus, We carried out microarray to investigate the down-stream target genes of TARDBP after silencing TARDBP in liver cancer cell SK-Hep1. To identify the role of TARDBP in hepatocellular carcinoma cell line, we performed microarray after knocking down TARDBP in hepatocellular carcinoma cell line (3 siLuc, 3 siTARDBP)				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Park	Park	Kim	Lee	
Person First Name	Yun-Yong	Yun-Yong	Sang	Ju-seog	
Person Mid Initials			B		
Person Email	yypark@mdanderson.org				
Person Affiliation	UT, MD Anderson Cancer Center				
Person Phone	7137458525				
Person Fax	7135634235				
Person Address	Systems Biology, UT, MD Anderson Cancer Center, 7435 Fannin St. , Houston, TX, USA				
Person Roles	submitter				
Protocol Name	P-GSE37640-1	P-GSE37640-3	P-GSE37640-4	P-GSE37640-2	P-GSE37640-5
Protocol Description	Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used. ID_REF = Illumina_ID VALUE = quantile normalized log2 signal	Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)	Labeled, amplified material (750 ng per array) was hybridized to a ver. 3 of the Illumina Human-Ht-12 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).	Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)	Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	KNOCKDOWN				
Experimental Factor Type	knockdown				
Publication Title	TARDBP regulates glycolysis in hepatocellular carcinomaby regulating PFKP through miR-520.				
Publication Author List	Park YY, Kim SB, Han HD, Sohn BH, Kim JH, Liang J, Lu Y, Mills GB, Sood AK, Lee JS				
PubMed ID	23389994				
Publication DOI	10.1002/hep.26310				
Comment[SecondaryAccession]	GSE37640				
Comment[GEOReleaseDate]	2013-04-22				
Comment[ArrayExpressSubmissionDate]	2012-04-27				
Comment[GEOLastUpdateDate]	2013-04-25				
Comment[AEExperimentType]	transcription profiling by array				
Comment[AdditionalFile:Data1]	GSE37640_non-normalized.txt				
SDRF File	E-GEOD-37640.sdrf.txt