Project description:Genome wide DNA methylation profiling of DNA extracted from formalin-fixed parffin embedded tumor samples from patients with primary intracranial sarcoma from Peru. The Illumina MethylationEPIC array was used to obtain DNA methylation profiles of 850.000 CpG sides
Project description:Total RNA were extracted from 5 primary melanoma and 5 nevus tissues, all of which were formalin-fixed and parrffin-embedded tissues.
Project description:Total RNA were extracted from 5 primary melanoma and 4 nevus tissues, all of which were formalin-fixed and parrffin-embedded tissues.
Project description:Genome wide DNA methylation profiling of dedifferentiated chondrosarcoma samples. Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue after manual macrodissection to ensure at least 10% tumor content, followed by bisulfite converstion. All samples were processed on the Infinium 850k array and scanned using the Illumina iScan, according to the manufacturer's recommended protocol.
Project description:Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies of 156 new patients using the Illumina DASL version 4 platform, plus 71 replicate samples from version 3 platform and 12 replicates from GSE32918. Then the patients were classified into BL and DLBCL by moleclar classifier proposed in the article.
Project description:Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 1311 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.
Project description:Comparison of gene expression profiles between a primary melanoma and an early metastatic specimen from the same patient will provide essential biological insight into early metastatic processes. The DASL (cDNA mediated annealing, selection, extension and ligation) assay has been used to generate gene expression data for 502 cancer-related genes from very small formalin-fixed sentinel node biopsy (SNB) melanoma samples, this data has been further compared with gene expression of the matched formalin-fixed primary melanoma. Tissue was sampled from twenty-five SNB deposits using laser capture microdissection. The mean number of genes detected using DASL with SNB samples was lower than when using a core of primary melanoma tumor (242 versus 434 genes). A large proportion of SNB samples failed (<240 genes detected) the assay (57.7%). Area of tissue microdissected, RNA concentration and qRT-PCR quality control did not predict performance of samples on the array but age of sampled tissue negatively correlated with number of genes detected (p=0.01). For samples that performed successfully, matched primary samples were available for 10 samples. Gene expression profiles correlated between all matched tumor pairs (Spearman’s rho 0.15-0.80, p<0.01), although a number of genes were differentially expressed between nodal and primary tumors in all tumor pairs. This study demonstrates that the DASL assay can be used to generate gene expression data from small formalin-fixed samples, but not consistently. Differentially expressed genes were identified across 10 matched primary and nodal tumor pairs suggesting that the DASL assay could be used to derive essential biological information about early metastasis.
Project description:Genome-wide DNA methylation screening was performed using the Infinium MethylationEPIC BeadChip in 49 fresh-frozen tissue samples and 31 formalin-fixed paraffin-embedded tissue samples obtained from surgically resected materials of patients with endometrioid endometrial cancer.
Project description:Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. All samples (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.
