Illumina HiSeq 2500 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
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
Steady state mice not treated 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. Total RNA was depleted of ribosomal RNA using Epibio’s universal bacteria ribo-zero kit, single version. Libraries were constructed using the NEBNext Ultra directional RNA Library Prep Kit (E7420L).
Experimental Factor: disease
none
Experimental Factor: treatment
none
LIBRARY_STRAND
not applicable