Project description:This study used laser capture microdissection to obtain paired tumor epithelium and stroma RNA samples from human pancreatic ductal adenocarcinoma (PDA) frozen sections. Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to model compartment-specific gene expression density on a genome-wide scale and build an algorithm for transcriptional devonvolution (ADVOCATE). RNA sequencing of macrodissected bulk PDA sections was performed on 15 samples in order to systematically compare TruSeq and NuGEN RNA-Seq libraries and (ii) correlate histopathological and molecular assessment of tumor composition.
Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs).
Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs). Invasive mammary carcinoma of the breast surgical resection specimens were laser capture microdissected for RNA extraction and hybridization to Affymetrix microarrays.
Project description:RNA-seq analysis of total RNA isolated from laser capture microdissected intestinal epithelium. The analysis aimed at characterizing the epithelial gene expression changes in IBD patients vs. healthy controls.
Project description:We performed gene expression profiling of laser capture microdissected normal non-neoplastic prostate (cystoprostatectomies) epithelial tissue and compared it to non-transformed and neoplastic low and high grade prostate epithelial tissue from radical prostatectomies, each with its immediately surrounding stroma.
Project description:Hydrogen sulfide (H2S) is a naturally occurring gas that is also associated with several industries. The potential for widespread human inhalation exposure to this toxic gas is recognized as a public health concern. The nasal epithelium is particularly susceptible to H2S-induced pathology. Injury to and regeneration of the nasal respiratory mucosa occurred in animals with ongoing H2S exposure suggesting that the regenerated respiratory epithelium undergoes an adaptive response and becomes resistant to further H2S induced toxicity. To better understand this adaptive response, twenty-four naive 10-week old male Sprague-Dawley rats were exposed to air or 200 ppm H2S in a nose-only exposure system for 3h/d for 1 or 5 consecutive days. Nasal respiratory epithelial cells at the site of injury and regeneration were laser capture microdissected and gene expression profiles were generated at time 3h, 6h, 24h, and 144h post initial exposure using the Affymetrix Rat Genome 430 2.0 microarray. Gene ontology enrichment analysis identified early gene changes in such functional categories as signal transduction, inflammatory/defense response, cell cycle, and response to oxidative stress. Later gene changes occurred in categories involved in cell cycle, DNA repair, transport, and micro-tubule-based movement. These data contribute to our understanding of the nasal epithelial cells? response to inhaled environmental toxicants. A better understanding of the H2S cytotoxicity mechanism will improve human risk assessment. Experiment Overall Design: Twenty-four naive 10-week old male Sprague-Dawley rats were exposed to air or 200 ppm H2S in a nose-only exposure system for 3h/d for 1 or 5 consecutive days. Nasal respiratory epithelial cells at the site of injury and regeneration were laser capture microdissected and gene expression profiles were generated at time 3h, 6h, 24h, and 144h post initial exposure using the Affymetrix Rat Genome 430 2.0 microarray.
Project description:Liquid chromatography mass spectrometry was used to study tumor matrisome from laser capture microdissected FFPE tissue sections of human neck and squamous cell carcinoma (HnSCC) xenograft grown in mouse.
Project description:Hydrogen sulfide (H2S) is a naturally occurring gas that is also associated with several industries. The potential for widespread human inhalation exposure to this toxic gas is recognized as a public health concern. The nasal epithelium is particularly susceptible to H2S-induced pathology. Injury to and regeneration of the nasal respiratory mucosa occurred in animals with ongoing H2S exposure suggesting that the regenerated respiratory epithelium undergoes an adaptive response and becomes resistant to further H2S induced toxicity. To better understand this adaptive response, twenty-four naive 10-week old male Sprague-Dawley rats were exposed to air or 200 ppm H2S in a nose-only exposure system for 3h/d for 1 or 5 consecutive days. Nasal respiratory epithelial cells at the site of injury and regeneration were laser capture microdissected and gene expression profiles were generated at time 3h, 6h, 24h, and 144h post initial exposure using the Affymetrix Rat Genome 430 2.0 microarray. Gene ontology enrichment analysis identified early gene changes in such functional categories as signal transduction, inflammatory/defense response, cell cycle, and response to oxidative stress. Later gene changes occurred in categories involved in cell cycle, DNA repair, transport, and micro-tubule-based movement. These data contribute to our understanding of the nasal epithelial cells? response to inhaled environmental toxicants. A better understanding of the H2S cytotoxicity mechanism will improve human risk assessment. Keywords: Time course