Conclusion

The aim of this project was to replicate the methods of the paper 'RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum', published by Xinglin Zhang et al.

The paper described that a gene cluster involved in purine biosynthesis was among the most upregulated genes when E. faecium was grown in human serum. This upregulation suggests that these genes contribute significantly to the bacterium's ability to proliferate in such conditions. This table of the top 5 most up-regulated genes highlights the importance of purine biosynthesis, as all of the five genes were involved in this process.

The top 5 upregulated genes, sorted by log2 fold change:

ID	Gene	Product	log2FoldChange	pvalue	padj
EJCDLKNP_00593	purS	Phosphoribosylformylglycinamidine synthase subunit PurS	9.5398617023098	0	0
EJCDLKNP_00592	purQ	Phosphoribosylformylglycinamidine synthase subunit PurQ	9.17932537423024	4.73329538080752e-85	2.27501109183133e-84
EJCDLKNP_00594	purC	Phosphoribosylaminoimidazole-succinocarboxamide synthase	9.01881644996045	1.14766784290543e-117	7.10844164966582e-117
EJCDLKNP_00591	purL	Phosphoribosylformylglycinamidine synthase subunit PurL	8.94826111153743	3.61830248804034e-90	1.82986206634229e-89
EJCDLKNP_00590	purF	Amidophosphoribosyltransferase	8.8327096770055	2.96677317419673e-144	2.1475148470571e-143

The paper also identified genes that were required for growth of E. faecium in serum, using a mutant transposon library. This part of the analysis had not been replicated, and therefore, we were not able to identify the pyrK_2, pyrF, purD, purH, and phosphotransferase system subunit (manY_2) as significant genes.