Project description:Matched normal lymph node, tumors and corresponding mucosal biopsies from 4 lung cancer patients were scrutinized on Affymetrix 250K-NspI array platform. Frequently deleted regions genes were identified based on the LOH call as per manufacturer's guidelines and normalization. Frequently deleted genes in the tumors and mucosa were identified though this approach
Project description:Matched normal lymph node, tumors and corresponding mucosal biopsies from 4 lung cancer patients were scrutinized on Affymetrix 250K-NspI array platform. Frequently deleted regions genes were identified based on the LOH call as per manufacturer's guidelines and normalization. Frequently deleted genes in the tumors and mucosa were identified though this approach Affymetrix 250K-NspI- SNP arrays were performed according to the manufacturer's directions on DNA extracted from lung cancer and corresponding mucosal biopsy specimens. LOH analysis was done to identify genes that are frequently deleted.
Project description:Diagnosing lung transplant rejection currently depends on histologic assessment of transbronchial biopsies (TBB) with limited reproducibility and considerable risk of complications. Mucosal biopsies are safer but not histologically interpretable. Microarray-based diagnostic systems for TBBs and other transplants suggest such systems could assess mucosal biopsies as well.
Project description:ALK fusion positive tumor constitutes a unique entitiy in lung adenocarcionmas. We compared the allelokaryotypes of ALK fusion positive and negative tumors with SNP array to get insight into the difference of genomic background of them. Copy number analysis with Affymetrix 250K SNP arrays of 35 ALK fusion positive and 95 ALK fusion negative lung adenocarcinomas was performed with annonymous references.
Project description:250k Sty, 250k Nsp, 250k Hind and 250k Xba Affymetrix SNP arrays for 50 leukemia remission samples used as controls for copy number analysis for GSE9109 and GSE9112. Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics *** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***
Project description:Microarrays were used to analyze the gene expression in endoscopic-derived intestinal mucosal biopsies from patients with inflammatory bowel disease (IBD) and controls Mucosal biopsies were obtained at endoscopy from the colon of 97 ulcerative colitis (UC), 8 Crohn's disease (CD) patients and 11 controls. The biopsies were taken at the most affected sites but at a distance of ulcerations. Disease activity was endoscopically assessed. Total RNA extracted from mucosal biopsies was used to analyze mRNA expression via Affymetrix Human Gene 1.0 ST arrays
Project description:Gene expression profiling of liver biopsies collected from 33 healthy liver donors ranging from 13 to 90 years old. The Affymetrix HG-U133 Plus 2.0 GeneChip platform was used to evaluate gene-expression. Total RNA (including miRNAs) was extracted using the mirVana miRNA Isolation Kit (Ambion); cDNA synthesis, biotin-labelled target synthesis, hybridization, staining and scanning were performed according to Affymetrix standard protocol. This dataset is part of the TransQST collection.
Project description:mRNA expression was assayed from bronchial epithelial cell samples from smokers with and without lung cancer. A subset of the samples (2 of the lung cancer samples and 3 of the no cancer samples) were pooled and underwent whole transcriptome sequencing. The goals were to compare whole transcriptome sequencing gene expression levels to gene expression levels derived from these samples run on the Affymetrix HGU133A 2.0 platform.
