Analysis of virus-derived small RNAs with high-throughput sequencing has been successful for detecting novel viruses in plants and invertebrates. However, the applicability of this method has not been demonstrated in fungi, although fungi were among the first organisms reported to utilize RNA silencing. Here, we used virus-infected isolates of the fungal species complex Heterobasidion annosum s...

Advances in sequencing technology have led to the development of many high-resolution methodologies that observe genomic activity and gene expression. This unit describes such an approach, native elongating transcript sequencing (NET-seq), which reveals the density of RNA polymerase across the Saccharomyces cerevisiae genome with single-nucleotide resolution. A procedure for capturing nascent R...

Several DNA/RNA sequencing strategies have been developed using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). In the reverse Sanger sequencing approach alpha-thiophosphate-containing NTPs are employed. Sequencing ladders are produced by the subsequent exonuclease cleavage, which is inhibited by the alpha-S-NTP at the 3' terminus. Here the reverse Sanger sequencing of...

High-throughput RNA-sequencing (RNA-seq) technologies are powerful tools for understanding cellular state. Often, it is of interest to quantify and summarize changes in cell state that occur between experimental or biological conditions. Differential expression typically assessed using univariate tests measure genewise shifts expression. However, these methods largely ignore transcriptional cor...

Hepatitis Delta virus (HDV) is a degenerate RNA virus or virusoid and a satellite of Hepatitis B virus (HBV). Three distinct genotypes are described for HDV; genotype I is distributed worldwide but other genotypes appear to be more restricted geographically. In the present study, an RT-nested PCR method was set up to detect delta infection from serum samples. Moreover, the target amplified sequ...

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the ...

Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of skin biology, but its utility is restricted by the requirement fresh samples, inadequate dissociation-induced cell loss or death, and activation during tissue digestion. Here, we profiled cells using single-nucleus (snRNA-seq) in parallel with scRNA-seq. We found that snRNA-seq identified more spatially functionally releva...

The sequencing of the transcriptomes of single-cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types and for the study of stochastic gene expression. In recent years, various tools for analyzing single-cell RNA-sequencing data have been proposed, many of them with the purpose of performing differentially expression analysis. In t...

Recent evidence demonstrates the power of RNA sequencing (RNA-Seq) for identifying valuable and urgently needed blood biomarkers and advancing both early and accurate detection of neurological diseases, and in particular Parkinson's disease (PD). RNA sequencing technology enables non-biased, high throughput, probe-independent inspection of expression data and high coverage and both quantificati...

The most popular RNA library used for RNA sequencing is the poly(A) captured RNA library. This library captures RNA based on the presence of poly(A) tails at the 3' end. Another type of RNA library for RNA sequencing is the total RNA library which differs from the poly(A) library by capture method and price. The total RNA library costs more and its capture of RNA is not dependent on the presenc...