RNA-seq results often contain a PCA or MDS plot. This StatQuest explains how these graphs are generated, how to interpret them, and how to determine if the plot is informative or not.
Read More »PathwaySeq – Pathway analysis for RNA-Seq data
A variety of pathway/gene-set approaches have been proposed to provide evidence of higher-level biological phenomena in the association of expression with experimental condition or clinical outcome. Among these approaches, it has been repeatedly shown that resampling methods are far preferable ...
Read More »Evaluating the Stability of RNA-Seq Transcriptome Profiles in Whole Blood Over Time
Researchers at the FDA have developed methods to evaluate the stability of rat whole blood expression obtained from RNA sequencing (RNA-seq) and assess changes in whole blood transcriptome profiles in experiments replicated over time. Expression was measured in globin-depleted RNA ...
Read More »Reducing error rates in third-generation sequencing technology
Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing ...
Read More »Understanding the differences between microarray and RNA-Seq technologies for measuring gene expression is necessary for informed design of experiments and choice of data analysis methods
Previous comparisons between microarrays and RNA-Seq have come to sometimes contradictory conclusions, which researchers from Princeton University suggest result from a lack of attention to the intensity-dependent nature of variation generated by the technologies. To examine this trend, they carried ...
Read More »deGPS – a tool for detecting differential expression in RNA-sequencing studies
The advent of the NGS technologies has permitted profiling of whole-genome transcriptomes (i.e., RNA-Seq) at unprecedented speed and very low cost. RNA-Seq provides a far more precise measurement of transcript levels and their isoforms compared to other methods such as ...
Read More »RNA extraction method, read length and sequencing layout (single-end versus paired-end) contribute strongly to variation between RNA-Seq samples
Sequencing-based gene expression methods like RNA-sequencing (RNA-seq) have become increasingly common, but it is often claimed that results obtained in different studies are not comparable owing to the influence of laboratory batch effects, differences in RNA extraction and sequencing library ...
Read More »The impact of quality filter for RNA-Seq
With the emergence of large-scale sequencing platforms since 2005, there has been a great revolution regarding methods for decoding DNA sequences, which have also affected quantitative and qualitative gene expression analyses through the RNA-Sequencing technique. However, issues related to the ...
Read More »Reduction of Gene Expression Variability from Single Cells to Populations follows Simple Statistical Laws
Recent studies on single cells and population transcriptomics have revealed striking differences in global gene expression distributions. Single cells display highly variable expressions between cells, while cell populations present deterministic global patterns. The mechanisms governing the reduction of transcriptome-wide variability ...
Read More »A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays
Understanding the differences between microarray and RNA-Seq technologies for measuring gene expression is necessary for informed design of experiments and choice of data analysis methods. Previous comparisons have come to sometimes contradictory conclusions, which may result from a lack of ...
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