Comment[ArrayExpressAccession]	E-GEOD-51276
MAGE-TAB Version	1.1						
Public Release Date	2013-10-01
Investigation Title	mRNA microarray analysis on HepG2 cells exposed to amorphous Silica Nanoparticles (SiO2-NP)						
Comment[Submitted Name]	mRNA microarray analysis on HepG2 cells exposed to amorphous Silica Nanoparticles (SiO2-NP)
Experiment Description	In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to amorphous Silica nanoparticles on Human hepatoma (HepG2) cells. We performed whole genome DNA microarray experiments using HepG2 cells exposed to  for 24h. We used whole genome microarrays to screen for global changed in HepG2 transcription profiles and with subsequent quantitative analysis conducted on selected genes. 24h SiO2-NP (100 mg/L) exposed HepG2 cells were used for total RNA extraction and hybridization on Affymetrix microarrays.						
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	choi	Choi	Chatterjee				
Person First Name	jinhee	Jinhee	Nivedita				
Person Email	jinhchoi@uos.ac.kr						
Person Affiliation	University of Seoul						
Person Phone	82-2-2210-5622						
Person Address	College of Urban Science, University of Seoul, 90 Jeonnong-dong, Dongdaemun-gu, seoul, South Korea						
Person Roles	submitter						
Protocol Name	P-GSE51276-1	P-GSE51276-4	P-GSE51276-5	P-GSE51276-7	P-GSE51276-2	P-GSE51276-3	P-GSE51276-6
Protocol Description	Affymetrix data were normalized, and summarized with the robust multi-average (RMA) method implemented in the Affymetrix Expression Console1.1 . To reduce noise for the significance analysis, the probesets called Absent by the MAS5 detection call on all arrays were filtered out. ID_REF =  VALUE = Log2 RMA signal intensity	About 300ng of total RNA from each sample was converted to cDNA, after amplification the double strands of cDNA was labelled with biotin-labeling (Ambion® WT Expression kit)	The amplified RNA was fragmented using 4.8μL of 5X fragmentation buffer (GeneChip® WT Terminal labeling kit; Affymetrix;P/N 900671) and hybridized to the gene containing over 33,290 transcripts, as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix). After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix)	The cells were exposed to 100 mg/L (prepared in MEM media from stock) dose for 24h	Cells were maintained in culture flasks with MEM media at 37oC with 5% CO2	Total RNA from control and SiO2 treated samples (100 mg/L for 24 h) were extracted by using RNA extraction kit (NucleoSpin, Macherey-Nagel)	GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE51276						
Comment[GEOReleaseDate]	2013-10-01						
Comment[ArrayExpressSubmissionDate]	2013-09-30						
Comment[GEOLastUpdateDate]	2013-10-02						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-51276.sdrf.txt