biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNicholes Candelariatranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-51656This microarray is an analysis of differentially expressed genes in three pancreatic ductal adenocarcinoma cell lines treated with LXR-agonist GW 3965. We first report that GW 3965 has antiproliferative effects in three PDAC cell lines. This microarray was designed to identify key mechanisms of the antiproliferative effect of LXR agonists within pancreatic cancer cell lines. Total RNA obtained from BxPC-3, MIA-PaCa-2, and PANC-1 pancreatic cancer cells grown in culture treated GW 3965 or ethanol (vehicle control) for 72 hours.biostudies-arrayexpressScaning - Standard Illumina scanning protocolSample Treatment - Cells were treated with 10 μM GW 3965 or ethanol (vehicle) for 72 hours prior to harvest and RNA isolation.Nucleic Acid Extraction - RNA was extracted using the Qiagen Rneasy Kit.Hybridization - Standard Illumina hybridization protocolGrowth Protocol - BxPC-3 cells were propogated in DMEM/F12 media, whereas MIA-PaCa-2 and PANC-1 cells were maintained in DMEM. All cell culture media was supplemented with 10% FBS.Labeling - cRNA were prepared and labeled with Cy3 dye using Illumina TotalPrep-96RNA Amplification Kit and Illumina Whole-Genome Gene Expression Direct Hybridisation KitMIAME ScoreOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsNicholes CandelariaChin-Yo LinData Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized PANC-1_Control2_H.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized MIA-PaCa-2_Control1_A.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized MIA-PaCa-2_GW1_D.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized BxPC-3_Control3_C.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized BxPC-3_GW3_F.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized MIA-PaCa-2_GW3_F.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized PANC-1_GW3_L.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized PANC-1_GW1_J.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized BxPC-3_GW1_D.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized MIA-PaCa-2_Control2_B.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized PANC-1_Control1_G.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized MIA-PaCa-2_GW2_E.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized BxPC-3_Control1_A.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized MIA-PaCa-2_Control3_C.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized BxPC-3_GW2_E.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized BxPC-3_Control2_B.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized PANC-1_Control3_I.Detection Pval =Data Transformation - Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set. ID_REF = VALUE = quantile normalized PANC-1_GW2_K.Detection Pval =falseAntiproliferative effects and mechanisms of liver X receptor ligands in pancreatic ductal adenocarcinoma cellsThis microarray is an analysis of differentially expressed genes in three pancreatic ductal adenocarcinoma cell lines treated with LXR-agonist GW 3965. We first report that GW 3965 has antiproliferative effects in three PDAC cell lines. This microarray was designed to identify key mechanisms of the antiproliferative effect of LXR agonists within pancreatic cancer cell lines. Total RNA obtained from BxPC-3, MIA-PaCa-2, and PANC-1 pancreatic cancer cells grown in culture treated GW 3965 or ethanol (vehicle control) for 72 hours.2014-04-15T00:00:00Z2023-09-06T12:31:30.687Z2022-03-15T05:59:10.098ZE-GEOD-51656GSE51656EFO_0002768