deep sequencing data set  (Temasek Laboratories)

Journal: mBio

Article Title: Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae

doi: 10.1128/mbio.03432-22

Figure Lengend Snippet: Specific mutations associated with high growth rate. (A) Screening fast-growing clones: five isolated clones per population (four S and one R) were tested per triplicate. The graph shows the average μ of each clones compared to the parental strain (black). Clones indicated in red were selected for further study. (B) The clones selected in panel A were subjected to growth curves by triplicate, and the percentage of variation of μ with respect to the parental strain is shown ( n = 4). The clones indicated with an arrow were subjected to deep sequencing. Statistical significance was analyzed by one-way ANOVA two-tailed test. Then, Tukey’s test was done to compare the mean values obtained for each strain. Statistically different means are indicated as follows: ***, P < 0.001; ****, P < 0.0001.

Article Snippet: The Illumina Deep Sequencing data sets are deposited at the GenBank SRA as BioProject PRJNA816505 .

Techniques: Clone Assay, Isolation, Sequencing, Two Tailed Test

Journal: Scientific Reports

Article Title: Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut

doi: 10.1038/srep15782

Figure Lengend Snippet: Bar plots above the heatmaps show the relative abundance of bifidobacteria in the analysed samples. Heatmaps in the upper part depict the coverage obtained by alignment of adult and infant fecal metagenomic data sets, or infant metatranscriptome data sets to predicted bifidobacterial GH-encoding genes. In order to compare results for datasets with different sizes, all coverage values were normalized as obtained from a 10 million read dataset. Heatmaps in the lower part of the image represent the coverage obtained by alignment of the same datasets to genes constituting the bifidobacterial pathways for carbohydrate degradation. Relevant GH genes and pathways involved in the metabolism of glycans are highlighted in red. Pathways designations are identical to those indicated in Fig. 1 .

Article Snippet: To this end we implemented a mapping-based pipeline to detect the presence and quantify the coverage of these gene categories annotated from the newly sequenced strains into the Illumina deep shotgun-sequenced metagenomic data sets derived from stool samples of the Human Microbiome Project (HMP) and into Illumina deep shotgun-sequenced metagenomic and metatranscriptomic data sets obtained from stool samples of nine healthy infants.

Techniques: