High throughput sequencing for the detection and characterization of RNA viruses

AH Fitzpatrick, A Rupnik, H O'Shea, F Crispie… - Frontiers in …, 2021 - frontiersin.org
This review aims to assess and recommend approaches for targeted and agnostic High
Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to …

What do we measure when we measure cell-associated HIV RNA

AO Pasternak, B Berkhout - Retrovirology, 2018 - Springer
Abstract Cell-associated (CA) HIV RNA has received much attention in recent years as a
surrogate measure of the efficiency of HIV latency reversion and because it may provide an …

Quantification of mRNA using real-time RT-PCR

T Nolan, RE Hands, SA Bustin - Nature protocols, 2006 - nature.com
The real-time reverse transcription polymerase chain reaction (RT-qPCR) addresses the
evident requirement for quantitative data analysis in molecular medicine, biotechnology …

Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-associated HIV-1 RNA

M Kiselinova, AO Pasternak, W De Spiegelaere… - PloS one, 2014 - journals.plos.org
Cell-associated (CA) HIV-1 RNA is considered a potential marker for assessment of viral
reservoir dynamics and antiretroviral therapy (ART) response in HIV-infected patients …

Measurable impact of RNA quality on gene expression results from quantitative PCR

J Vermeulen, K De Preter, S Lefever… - Nucleic acids …, 2011 - academic.oup.com
Compromised RNA quality is suggested to lead to unreliable results in gene expression
studies. Therefore, assessment of RNA integrity and purity is deemed essential prior to …

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

C Plessy, N Bertin, H Takahashi, R Simone… - Nature …, 2010 - nature.com
Large-scale sequencing projects have revealed an unexpected complexity in the origins,
structures and functions of mammalian transcripts. Many loci are known to produce …

A comparison of transcriptomic profiles in endometrium during window of implantation between women with unexplained recurrent implantation failure and recurrent …

J Huang, H Qin, Y Yang, X Chen, J Zhang… - …, 2017 - rep.bioscientifica.com
The endometrium becomes receptive to the embryo only in the mid-luteal phase, but not in
the other stages of the menstrual cycle. Endometrial factors play an important role in …

The endogenous opioid system in human alcoholics: molecular adaptations in brain areas involved in cognitive control of addiction

I Bazov, O Kononenko, H Watanabe, V Kuntić… - Addiction …, 2013 - Wiley Online Library
The endogenous opioid system (EOS) plays a critical role in addictive processes. Molecular
dysregulations in this system may be specific for different stages of addiction cycle and …

Exploring the impact of primer length on efficient gene detection via high-throughput sequencing

J Micheel, A Safrastyan, F Aron, D Wollny - Nature Communications, 2024 - nature.com
Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing
protocols for this initial stage is critical for effective target detection, particularly when …

A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study

K Graeber, A Linkies, ATA Wood… - The Plant …, 2011 - academic.oup.com
Comparative biology includes the comparison of transcriptome and quantitative real-time RT-
PCR (qRT-PCR) data sets in a range of species to detect evolutionarily conserved and …