Journal: PLoS ONE

Article Title: Deep Annotation of Populus trichocarpa microRNAs from Diverse Tissue Sets

doi: 10.1371/journal.pone.0033034

Figure Lengend Snippet: Clustering of smallRNA sequencing runs by miRNA expression. [miRNA expression = (Raw Abundance)/(Number of Mappable Reads)×1,000,000] reveals that xylem and mechanically treated xylem (MTX) are most similar. MATLAB clustergram algorithm was used for expression clustering.

Article Snippet: Hierarchical clustering of the four sequenced datasets based on annotated miRNAs and expression levels of these miRNAs was performed using MATLAB's Clustergram algorithm ( ) , .

Techniques: Sequencing, Expressing

Journal: PLoS Pathogens

Article Title: Para -cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria

doi: 10.1371/journal.ppat.1007191

Figure Lengend Snippet: a) Principle component analysis (PCA) score plot based on the 1 H NMR spectra of the three C . difficile strains (630Δ erm (black), hpdC ::CT (red) and the complemented mutant ( hpdC ::CT::p hpdC-A ) in (blue), grown in monoculture (circle symbol) or in competitive co-culture with intestinal commensal species, E . coli (square), K . oxytoca (triangle) and B . thetaiotaomicron (star), in BHIS media supplemented with 0.2% p- HPA. b) Metabolite clustergram represented as a heatmap of Z -scores of the 1 H NMR peak integrals, derived from the quantity of six main metabolites driving the separation between the samples (observed on the loading plots of the model) and a dendrogram showing the hierarchical clustering of the samples. The culture conditions, bacterial strains and p -HPA concentration are colour coded in a key on the heatmap.

Article Snippet: These metabolite peak integrals were used to construct a clustergram in Matlab using the clustergram script.

Techniques: Mutagenesis, Co-Culture Assay, Derivative Assay, Concentration Assay