Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008).
Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008). For this study, 4 experimental Virochip microarrays derived from tissue and swabs from affected titi monkeys were analyzed. We also used 18 Virochip microarrays derived from sera from healthy random human blood donors as a negative background set for Z-score analysis (see Chiu, et al., Clin Infect Dis, 2006). Raw Agilent microarray .txt files are background normalized and the 19,058 70-mer viral probes are then selected and displayed as columns in the processed data table.
Project description:CpG island methylation profiling of human cholangiocarcinoma, ECC and ICC, cases compared to matched normal controls or to pools of corresponding normal controls. Goal was to identify cholangiocarcinoma-specific differentially methylated regions (DMRs). Highly methylated DNA from cases and controls was enriched by methyl CpG-immunoprecipitation (MCIp) and co-hybridized. DMRs were defined by stepwise stringent criteria such as selecting top 5% vicinal array probes only. ECC- and ICC-specific and common DMRs were identified.
Project description:CpG island methylation profiling of human cholangiocarcinoma, ECC and ICC, cases compared to matched normal controls or to pools of corresponding normal controls. Goal was to identify cholangiocarcinoma-specific differentially methylated regions (DMRs).
