biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsyuriko saikitranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-39493We performed microarray analyses before and after induction of S100A4 using PCI-35 and PCI-43, and identified 72 and 18 genes that were two fold or more commonly upregulated or downregulated, respectively, in these two cell lines. Using two cell lines, PCI-35 and PCI-43, transfected with S1004A expression construct, we studied mRNA transcription levels by microarray analysis to see if there are any of the key molecules for malignant phenotype.biostudies-arrayexpressHybridization - 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.Labeling - Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp labeling kit one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.Sample Processing - To overexpress S100A4 protein, the expression vector was transfected in pancreatic cancer cell lines using lipofectamine 2000 reagent (Invitrogen) according to the methods by the suppliers. An empty pcDNA6/Myc-His plasmid was also transfected as a control.Growth Protocol - Cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.Nucleic Acid Extraction - RNA was prepared using the RNeasy Mini Kit (Qiagen, Studio City, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray Designsyuriko saikiAkira HoriiKeisuke SatoHitoshi SekineYuriko SaikiAssay Data Transformation - ID_REF = VALUE = processed Cy3 signal intensity (Agilent gProcessedSignal)Feature Extraction - The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.Image Adquisition - Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).falseGene expression profiling after S1004A inductionWe performed microarray analyses before and after induction of S100A4 using PCI-35 and PCI-43, and identified 72 and 18 genes that were two fold or more commonly upregulated or downregulated, respectively, in these two cell lines. Using two cell lines, PCI-35 and PCI-43, transfected with S1004A expression construct, we studied mRNA transcription levels by microarray analysis to see if there are any of the key molecules for malignant phenotype.2012-12-31T00:00:00Z2023-09-05T14:12:59.461Z2021-10-01T17:17:01ZE-GEOD-39493GSE39493EFO_0002768