title: 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
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 intraperitoneal injection of anti-IL10 receptor antibody at days 0 and 7 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).
attributes.tag: Experimental Factor: disease
attributes.value: colitis
attributes.tag: Experimental Factor: treatment
attributes.value: Helicobacter hepaticus gavage (10E8 bacteria) with Intraperitoneal injection of 10mg anti-IL10R antibody on days 0 and 7
attributes.tag: LIBRARY_STRAND
attributes.value: not applicable