title: Illumina MiSeq paired end sequencing; 16S rDNA sequencing of Ldlr-/- mouse gut microbiomes
design: 16S rDNA sequencing of Ldlr-/- mouse gut microbiomes
library_name: Sample 9_p
library_construction_protocol: Seven-week-old male Ldlr-/- mice were purchased from Jackson Laboratories and maintained on a 12-h light/ 12-h dark cycle at a temperature of 22oC with 50% humidity.  Following one week of acclimation, mice were randomly divided into 4 groups (n=10).  Mice were fed either a control high cholesterol diet containing 8% cellulose as the fiber source (2 groups; n=10 each) or a prebiotic containing high cholesterol diet with 8% of inulin as the fiber source (2 groups; n=10 each).  At weeks 2 and 4, mice received either 1 µmol/kg of PCB 126 (AccuStandard, CT, USA) or safflower oil vehicle (Dyets, Bethlehem, PA, USA) via oral gavage.  At the end of the study mice were fasted for 16 h, anesthetized and blood was collected via retro-orbital bleed.  Cecum samples were collected, snap frozen in liquid nitrogen, and stored at -80oC until analysis. DNA extraction and 16S sequencing was conducted by the Environmental Sample Preparation and Sequencing Facility (ESPSF) at Argonne National Laboratory and analyzed by the program Quantitative Insights Into Microbial Ecology (QIIME). DNA was extracted using PowerSoil 96-well DNA Isolation Kit (MoBio, Carlsbad, CA, USA) PCR amplicon libraries targeting the 16S rRNA encoding gene present in metagenomic DNA are produced using a barcoded primer set adapted for the Illumina HiSeq2000 and MiSeq
attributes.tag: Experimental Factor: compound
attributes.value: none
attributes.tag: Experimental Factor: diet
attributes.value: cellulose