Comment[ArrayExpressAccession] E-GEOD-66361 MAGE-TAB Version 1.1 Public Release Date 2015-08-27 Investigation Title Analysis of the gene expression profile in cutaneous squamous cell carcinoma cells after EphB2 knockdown Comment[Submitted Name] Analysis of the gene expression profile in cutaneous squamous cell carcinoma cells after EphB2 knockdown Experiment Description The role of Eph/ephrin signaling in numerous biological processes has been established. However, Eph/ephrin signaling has been shown to have complex role in tumor progression. The role of EphB2 receptor in the progression of cutaneous squamous cell carcinoma (cSCC) has not been studied before. EphB2 is significantly overexpressed in cSCC cells compared with normal human epidermal keratinocytes (NHEKs). We used microarray based global gene expression profiling to study the effect of EphB2 knockdown on the expression of different genes in cSCC cells. cSCC cell lines (n=3) were transfected with either control or EphB2 siRNA (75 nM) and incubated for 72 hours. Total RNA was extracted and processed expression profiling with GeneChip 3’ IVT Express Kit according to manufacturer’s protocol. 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 Nissinen Frashchian Nissinen Kähäri Person First Name Liisa Mehdi Liisa Veli-Matti Person Email liisa.nissinen@utu.fi Person Affiliation University of Turku Person Phone +35823337021 Person Address Dermatology, University of Turku, Tykistökatu 6 A, Turku, Finland Person Roles submitter Protocol Name P-GSE66361-1 P-GSE66361-5 P-GSE66361-6 P-GSE66361-2 P-GSE66361-3 P-GSE66361-4 P-GSE66361-7 Protocol Description Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control GeneTitan® hybridization process and in summarizing probe cell intensity data. After hybridization quality was checked with AGCC and Expression ConsoleTM 1.1. The data were normalized to remove variation between samples caused by non-biological reasons. Normalization of the array was performed using GCRMA . Data were subjected for statistical analysis with Chipster (CSC-IT Center for Science, Ltd, Espoo, Finland). R package limma was used for performing the statistical testing between the groups. ID_REF = VALUE = log2 RMA signal Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol for GeneChip® expression analysis techinical manual. Samples were hybridized to GeneChip® Human Genome U219 16-array plate with specific protocols for using the GeneTitan® Hybridization, Wash and Stain Kit for 3’ IVT Array Plates. cSCC cell lines were transfected with control or EphB2 siRNA (75 nM) and incubated for 72 hours at 37C. cSCC cell lines were cultured at 37C to reach 60-70% confluency. 72 hours after transfections, RNAs were extracted according to the manufacturer's instruction and eluted in streile water ( Qiagen Rneasy kit, Qiagen GmbH, Hilden, Germany) GeneTitan® Instrument was used to scan the arrays. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name protocol Experimental Factor Type protocol Publication Title EphB2 Promotes Progression of Cutaneous Squamous Cell Carcinoma. Publication Author List Farshchian M, Nissinen L, Siljam�ki E, Riihil� P, Toriseva M, Kivisaari A, Ala-Aho R, Kallajoki M, Ver�j�nkorva E, Honkanen HK, Heljasvaara R, Pihlajaniemi T, Gr�nman R, Peltonen J, Peltonen S, K�h�ri VM PubMed ID 25789706 Publication DOI 10.1038/jid.2015.104 Comment[SecondaryAccession] GSE66361 Comment[GEOReleaseDate] 2015-08-27 Comment[ArrayExpressSubmissionDate] 2015-02-27 Comment[GEOLastUpdateDate] 2015-08-28 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-66361.sdrf.txt