Comment[ArrayExpressAccession]	E-GEOD-78501
MAGE-TAB Version	1.1					
Public Release Date	2016-08-22
Investigation Title	Gene expression profiling of genes differentially expressed by oral carcinoma Ca9-22 and SLPI-deficient Ca9-22 (ΔSLPI) cells					
Comment[Submitted Name]	Gene expression profiling of genes differentially expressed by oral carcinoma Ca9-22 and SLPI-deficient Ca9-22 (ΔSLPI) cells
Experiment Description	We used the myoma model in conjunction with gene expression profiling with microarray data as an efficient tool for high throughput analysis and to screen for differentially expressed genes. Our aim was to identify candidates playing an important role in SLPI and/or MMP-promoted tumor invasion by comparing oral carcinoma Ca9-22 cells, which highly express secretory leukocyte protease inhibitor (SLPI) gene, with SLPI-deficient Ca9-22 cells. In oral carcinoma Ca9-22 and SLPI-deficient Ca9-22 (ΔSLPI) samples, gene expression profiling was performed with the Affymetrix Human Genome U133 Plus 2.0 Array. Two arrays for 2 cell lines were analyzed.					
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	Fukushima	Mikami	Fukushima			
Person First Name	Atsushi	Yoshikazu	Atsushi			
Person Email	atsushi.fukushima@riken.jp					
Person Affiliation	RIKEN					
Person Address	Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Japan					
Person Roles	submitter					
Protocol Name	P-GSE78501-1	P-GSE78501-4	P-GSE78501-5	P-GSE78501-2	P-GSE78501-3	P-GSE78501-6
Protocol Description	The data were analyzed with Bioconductor 'simpleaffy' package using RMA as normalization method. ID_REF =  VALUE = RMA signal intensity	Biotin-labeled cRNA was synthesized by in vitro transcription using the BioArray high-yield RNA transcript labeling system (ENZO, Farmingdale, NY, USA).	Biotin-labeled cRNA was added to the fragmentation buffer (Affymetrix), and was heated for 35 min at 95°C. Fragmented cRNA (10 μg) was hybridized to GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix).	Ca9-22 cells were obtained from RIKEN BRC (Ibaraki, Japan). SLPI-deficient (Δ) Ca9-22 cells were generated as previously described (Mikami et al. Mol Immunol, 2015). Cells were maintained in α-Minimal Essential Medium (Wako, Tokyo, Japan) containing 10% fetal bovine serum (Japan Bio Serum, Tokyo, Japan) and 1% penicillin-streptomycin (Wako) at 37°C in an atmosphere containing 5% CO2.	Total RNA was extracted using RNeasy kits (Qiagen, Valencia, CA, USA) according to the manufacturer's instruction.	GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	genotype					
Experimental Factor Type	genotype					
Publication Title	Human uterus myoma and gene expression profiling: A novel in vitro model for studying secretory leukocyte protease inhibitor-mediated tumor invasion.					
Publication Author List	Mikami Y, Fukushima A, Komiyama Y, Iwase T, Tsuda H, Higuchi Y, Hayakawa S, Kuyama K, Komiyama K					
PubMed ID	27238568					
Publication DOI	10.1016/j.canlet.2016.05.028					
Comment[SecondaryAccession]	GSE78501					
Comment[GEOReleaseDate]	2016-08-22					
Comment[ArrayExpressSubmissionDate]	2016-02-25					
Comment[GEOLastUpdateDate]	2016-10-28					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-78501.sdrf.txt