BACKGROUND Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approach...

Quantitative measurement of transcription rates in live cells is important for revealing mechanisms of transcriptional regulation. This is particularly challenging when measuring the activity of RNA polymerase III (Pol III), which transcribes growth-promoting small RNAs. To address this issue, we developed Corn, a genetically encoded fluorescent RNA reporter suitable for quantifying RNA transcr...

Human immunodeficiency virus type 1 (HIV-1) RNA and p24 antigen concentrations were determined in plasma samples from 169 chronically infected patients (median CD4 cell count, 140 cells/microL; range, 0-1500 cells/microL). p24 quantification involved heat-mediated immune complex dissociation and tyramide signal amplification-boosted ELISA, which has a diagnostic sensitivity similar to that of R...

Next-generation sequence based transcriptome methodologies (broadly referred to as RNA-seq) were initially developed in 2007 for massively parallel short read sequencing platforms. RNA-seq involves purification of RNA, followed by either selection of poly-A(+) RNA or depletion of ribosomal RNA. RNA is then converted into cDNA by one of two methods; 1) random priming, followed by cDNA fragmentat...

Next-generation sequence based transcriptome methodologies (broadly referred to as RNA-seq) were initially developed in 2007 for massively parallel short read sequencing platforms. RNA-seq involves purification of RNA, followed by either selection of poly-A(+) RNA or depletion of ribosomal RNA. RNA is then converted into cDNA by one of two methods; 1) random priming, followed by cDNA fragmentat...

Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to evaluate the comparability of measurements...

The ability to monitor and perturb RNAs in living cells would benefit greatly from a modular protein architecture that targets unmodified RNA sequences in a programmable way. We report that the RNA-binding protein PumHD (Pumilio homology domain), which has been widely used in native and modified form for targeting RNA, can be engineered to yield a set of four canonical protein modules, each of ...