Nathalie Pochet

TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.

TL;DR: Findings suggest that IFN-Is produced in the CNS function in combination with metabolites derived from dietary tryptophan by the gut flora to activate AHR signaling in astrocytes and suppress CNS inflammation.

TL;DR: This work shows that S. cerevisiae is also a model for the evolution of cooperative behavior by revisiting flocculation, a self-adherence phenotype lacking in most laboratory strains, and expresses the gene FLO1, which is driven by one of a few known "green beard genes," which direct cooperation toward other carriers of the same gene.

TL;DR: It is found that the RNase H method performed best for chemically fragmented, low-quality RNA, and was confirmed through analysis of actual degraded samples, and can even effectively replace oligo(dT)-based methods for standard RNA-seq.

TL;DR: This protocol describes the use of the Trinity platform for de novo transcriptome assembly from RNA-Seq data in non-model organisms and presents Trinity’s supported companion utilities for downstream applications, including RSEM for transcript abundance estimation and R/Bioconductor packages for identifying differentially expressed transcripts across samples.