Project description:Genome-wide expression assay of S. alterniflora individuals from populations (4 from Louisiana, 2 from Mississippi) either exposed or unexposed to the Deepwater Horizon oil spill
Project description:Histology in the mesentery pointed to altered blood vessels. This experiment was designed to define the differences in gene expression in vessels from Crohn's disease versus controls. Crohn's disease was separately evaluated in inflamed (central disease) areas and in adjacent noninflamed areas.
Project description:Histology in the mesentery pointed to altered blood vessels. This experiment was designed to define the differences in gene expression in vessels from Crohn's disease versus controls. Crohn's disease was separately evaluated in inflamed (central disease) areas and in adjacent noninflamed areas. Laser capture microdissection was carried out on Carnoy's fixed mesenteric samples, comparing normal arteries or veins with Crohn's inflamed or nonifnlamed arteries or veins.
Project description:In this study we characterize the gill transcriptome changes in Gulf killifish (Fundulus grandis) that coincide with controlled laboratory-based exposure to various concentrations of experimentally-weathered south Louisiana crude oil. Gill transcription was contrasted between doses and across timepoints following dosing.
Project description:In this study we characterize the liver transcriptome changes in Gulf killifish (Fundulus grandis) that coincide with controlled laboratory-based exposure to various concentrations of experimentally-weathered south Louisiana crude oil. Liver transcription was contrasted between doses and across timepoints following dosing.
Project description:Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and FFPE tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis.
Project description:In this study, we report a broad analysis of central tumor samples (C), from both Glioblastoma long term survivors (LT) and short term ones (ST), integrated by the same analysis performed on peritumoral areas (P) from the same patients. We provide data from SAGE analysis performed with deep sequencing.
