Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp mutant strain and a Bacteroides fragilis NCTC 9343 delta-lfg mutant strain, each as compared to the wild-type strain. The mutations engineered into these strains interfere with B. fragilis protein glycosylation.
Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 double mutant compared to the wild-type strain. Keywords: expression analysis A six chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343 and three separate cultures of a double mutant strain, Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2, in which ungD1 (BF1706) and ungD2 (BF2848) are deleted. Each chip measures the expression level of 4,302 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
Project description:5 conditions for RNA-sequencing: Mono-culture biofilms of C. difficile WT, C. difficile luxS mutant (insertional ClosTron mutant as described in DOI: 10.1128/JB.01980-12), B. fragilis (PRJEB29695), and co-cultures biofilms of C. difficile WT and luxS mutant with B. fragilis. These were used to compare differences between C. difficile WT and luxS during mono-culture biofilms, as well transcriptomic differences for both C. difficile and B. fragilis during co-culture.
Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH triple mutant, compared to the wild-type strain. The mutations engineered into this strain render it acapsular. The mutants analyzed in this study are further described in Coyne, M. J., M. Chatzidaki-Livanis, L. C. Paoletti, and L. E. Comstock. 2008. Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. PNAS 105(35):13098-13103 (PID 18723678). A six chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343 and three separate cultures of a triple mutant strain, Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH, in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely. Each chip measures the expression level of 4,302 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
Project description:To elucidate whether Enterotoxigenic Bacteroides fragilis (ETBF) plays a role in intestinal inflammation and colorectal carcinogenesis, a RNA-seq analysis was performed to compare the microRNA profiles of ETBF treated HCT116 colorectal cancer cell lines.
