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. All samples in this study (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.
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.
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 (GSE48644) and formalin-fixed paraffin embedded (FFPE; this study) samples using two-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 one-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.
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 RNA-seq (polyA-enrichment protocol). All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (ribo-depletion protocol) in order to determine the effect of the technology on gene expression profiles.
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 RNA-seq (ribo-depletion protocol). All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (polyA-enrichment protocol) in order to determine the effect of the technology on gene expression profiles.
Project description:We used Illumina microarrays to profile RNA expression in formalin-fixed paraffin-embedded (FFPE) samples of 22 metastatic or advanced RCC cases.
