In contrast to any conventionally performed end-point analysis based on counting numbers of dead/immobile specimens we performed a fully automated time-resolved video data analysis to dynamically assess the effect of a reference toxicant on selected behavioral parameters.
To assess the ability of the STAMP assay to discriminate similar specimens, we performed replicate analyses using DNA isolated from M091 cells that were either untreated or treated with the hypomethylating agent, 5-aza-2'-deoxycytidine (decitabine).
Finally, to prove that this interaction occurred also in clinical tumor specimens we performed ChIP to assess binding of ERG to the EZH2 promoter in ERGhigh and NoETS samples (Fig. 3G).
For subsequent specimens we performed FISH on 2+ and 3+ IHC subgroups.
By combining signal from normal and tumor specimens, we performed a sensitivity analysis, evaluating how normal contamination affected tumor classifiers.
To detect FCoV in clinical specimens, we performed RT-PCR using a random primer plus a single PCR targeted nsp14 constructed in the present study.
To ascertain whether sialyl-T antigens were also expressed in the normal urothelium and bladder tumor specimens, we performed a PNA dot blot analysis.
To further evaluate the sensitivity of PCR on unextracted clinical specimens, we performed real-time PCR analysis on dilutions of previously quantified stocks of patient-derived HSV particles.
On a large cohort of breast cancer specimens we performed a first systematic expression analysis of FOXM1 on both mRNA and protein level and subsequently studied FOXM1 expression with respect to clinicopathological parameters and patients' survival data.
To detect SARS-CoV in stool, urine, and respiratory specimens, we performed reverse transcriptase polymerase chain reaction (RT-PCR), using primers targeted to the polymerase and nucleocapsid genes of the SARS-CoV genome, as described elsewhere (2, Emery et al., unpub data).
