ABSTRACT: Laboratory strain poliovirus was hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-polio probes was evaluated. Specificity of the probe design was determined. Keywords: control study: target detection and specificity
Project description:Co-hybridization of Adenovirus type 40 and 41 to test probe specificity for closely related viral targets. ATCC strains of Adenovirus type 40 and 41 were hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-adenovirus 40 and 41 probes was evaluated. Specificity of the probe design was determined between closely related members of the same virus family. Keywords: control study: target detection and specificity
Project description:Co-hybridization of Adenovirus type 40 and 41 to test probe specificity for closely related viral targets. ATCC strains of Adenovirus type 40 and 41 were hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-adenovirus 40 and 41 probes was evaluated. Specificity of the probe design was determined between closely related members of the same virus family. Keywords: control study: target detection and specificity 2 lab strains of adenovirus (type 40 and 41) were extracted directly from ATCC samples. Viral DNA was was extracted and labeled with Cy3 and Cy5 dyes for Adenovirus type 40 and 41 respectively.
Project description:The central goal of the project is to define, experimentally verify, and systematically annotate pathways of endocrine disruption, as a proof of concept of mapping pathways of toxicity by systems toxicology. Experiments were designed to detect possible genomic heterogeneity and genetic drifts within MCF-7 obtained from ATCC (HTB-22, lot number 59388743, passage 147).
2016-04-29 | GSE80760 | GEO
Project description:Poliovirus Shedding after Sequential Immunization of Sabin-Strain Inactivated Polio Vaccines and Oral Attenuated Polio Vaccines
Project description:miRNAs are excellent tumor biomarkers because of their cell-type specificity and abundance. However, many miRNA detection methods, such as real-time (RT)-PCR, obliterate valuable visuospatial information in tissue samples. To enable miRNA visualization in formalin-fixed paraffin-embedded (FFPE) tissues, we developed multicolor miRNA fluorescence in situ hybridization (FISH). For proof-of-concept, we differentiated two skin tumors, namely Basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), with overlapping histologic features but distinct cellular origins. Using sequencing-based miRNA profiling and discriminant analysis, we identified tumor-specific miRNAs (miR-205 and miR-375) in BCC and MCC respectively. We addressed three major shortcomings in miRNA FISH, identifying optimal conditions for miRNA fixation and rRNA retention using model compounds and HPLC analyses, enhancing signal amplification and detection by increasing probe-hapten linker lengths, and improving probe specificity using shortened probes with minimal rRNA sequence complementarity. We validated our method on 4 BCC and 12 MCC tumors. Amplified miR-205 and miR-375 signals were normalized against directly detectable reference rRNA signals. Tumors were classified using pre-defined cut-off values; all were correctly identified in blinded analysis. We established a reliable miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues 6 MCC samples 2 normal skin samples were profiled with Agilent miRNA array platform
Project description:miRNAs are excellent tumor biomarkers because of their cell-type specificity and abundance. However, many miRNA detection methods, such as real-time (RT)-PCR, obliterate valuable visuospatial information in tissue samples. To enable miRNA visualization in formalin-fixed paraffin-embedded (FFPE) tissues, we developed multicolor miRNA fluorescence in situ hybridization (FISH). For proof-of-concept, we differentiated two skin tumors, namely Basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), with overlapping histologic features but distinct cellular origins. Using sequencing-based miRNA profiling and discriminant analysis, we identified tumor-specific miRNAs (miR-205 and miR-375) in BCC and MCC respectively. We addressed three major shortcomings in miRNA FISH, identifying optimal conditions for miRNA fixation and rRNA retention using model compounds and HPLC analyses, enhancing signal amplification and detection by increasing probe-hapten linker lengths, and improving probe specificity using shortened probes with minimal rRNA sequence complementarity. We validated our method on 4 BCC and 12 MCC tumors. Amplified miR-205 and miR-375 signals were normalized against directly detectable reference rRNA signals. Tumors were classified using pre-defined cut-off values; all were correctly identified in blinded analysis. We established a reliable miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues
2013-03-14 | GSE45146 | GEO
Project description:Proof of concept of massively PCR barcoding
Project description:Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing Proof-of-concept of RPL in S. cerevisiae and H. sapiens tissue culture
Project description:This study proposes to determine the safety of the administration of E7820 plus cetuximab and explore the MTD of the combination in a Phase Ib study. In addition, the efficacy of this combination will be explored in patients with colorectal cancer in the Phase II proof of concept phase of the study.