Project description:Seasonality of planktonic freshwater ciliates with a focus on twelve representatives: Are estimations based on V9 regions of the 18S rRNA gene comparable to classical analyses of morphospecies?
Project description:Microarray analysis of miRNA—Two micrograms of total RNA was extended at the 3′ terminus with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to the target microRNA (miRBase, http://mirbase.org) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using photogenerated reagent chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µl 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After RNA hybridization, tag-conjugating Cy5 dye was circulated through the microfluidic chip for dye staining. Fluorescence images were collected by using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
Project description:We profiled and quantitated miRNAs in two skin tumors (Basal cell carcinoma and Merkel cell carcinoma) and identified tumor-specific miRNAs. We used these tumor-specific miRNAs to guide development of miRNA fluorescence in situ hybridization.
2013-06-28 | GSE34137 | GEO
Project description:Applicability of live-fluorescence in situ hybridization (Live-FISH) on soil microbiomes
Project description:We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics Laboratories using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing to glean insights into potential mechanisms of formation.
Project description:Probe panel for 94 genes designed using Resolve Biosciences proprietary design software, as reported in table S4 of the manuscript . Molecular Cartography (100-plex combinatorial single molecule fluorescence in-situ hybridization)
