organism: mouse gut metagenome
description: Protocols: 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: ENA-FIRST-PUBLIC
attributes.value: 2020-02-27T04:03:39Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2020-02-17T11:40:17Z
attributes.tag: External Id
attributes.value: SAMEA6564971
attributes.tag: INSDC center name
attributes.value: UNIVERSITY OF KENTUCKY
attributes.tag: INSDC first public
attributes.value: 2020-02-27T04:03:39Z
attributes.tag: INSDC last update
attributes.value: 2020-02-17T11:40:17Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8798:Sample 16
attributes.tag: age
attributes.value: 7
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: diet
attributes.value: cellulose
attributes.tag: genotype
attributes.value: Ldlr-/-
attributes.tag: organism part
attributes.value: feces
attributes.tag: sample name
attributes.value: E-MTAB-8798:Sample 16
attributes.tag: scientific_name
attributes.value: mouse gut metagenome
attributes.tag: sex
attributes.value: male
attributes.tag: strain
attributes.value: C57BL/6