title: Illumina HiSeq 2000 paired end sequencing; Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
design: Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression
library_construction_protocol: oral gavage of helicobacter hepaticus at 1E8 bacterium on days 0,1 and 2 For simultaneous DNA and RNA extraction, pellets were dissolved in 500 ul extraction buffer (200 mM NaCl, 20 mM EDTA, 4 M guanidine thiocyanate, 1 % (v/v) β-mercaptoethanol) and 210 ul 20 % (w/v) SDS and lysed with a bead beater twice for 2 minutes employing Lysing Matrix E tubes (MP Biomedicals). Samples were centrifuged at 8000 g for 5 minutes and the supernatant was diluted with 3 volumes of lysing buffer (ZR-Duet DNA/RNA Miniprep Kit, Zymo Research). DNA and RNA were further extracted employing the ZR-Duet DNA/RNA Miniprep Kit according to the manufacturer’s instructions. Libraries were prepared using the PrepX ILM 32i DNA Library Kit
attributes.tag: Experimental Factor: disease
attributes.value: none
attributes.tag: Experimental Factor: treatment
attributes.value: Helicobacter hepaticus oral gavage (1E8 bacteria on days 0, 1 and 2)
attributes.tag: LIBRARY_STRAND
attributes.value: not applicable