characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-05-01T17:03:29Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-05-16T18:32:19Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104033724
characteristics.characteristic: External Id
characteristics.text: unspecified
characteristics.characteristic: INSDC center name
characteristics.text: 2018-05-01T17:03:29Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-05-16T18:32:19Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1697617
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5720:12480
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Protocols: Mice were housed in an enhanced barrier specific pathogen-free facility under a strict 12-hour light cycle and fed irradiated chow diet (PicoLab Rodent Chow 20, Purina Mills). Mice were maintained on a C57BL/6 background. A heterozygous x heterozygous breeding scheme was used to generate Atg16l1 T300A and wildtype littermate control mice. All study protocols were approved by the Washington University Animal Studies Committee. A set of 4- to 6-week-old Atg16l1 T300A and littermate mice were exposed to mainstream cigarette smoking 4 cigarettes/day, 5 days/week, for 2 weeks, using Kentucky research cigarette 3R4F in a smoking chamber. These mice were used as microbiota donors. A separate set of similar aged mice that were not exposed to cigarette smoking was used as microbiota recipients. The microbiota recipients were pre-treated with broad spectrum antibiotics (vancomycin, neomycin, ampicillin, and metronidazole) for a week prior to cohousing to eradicate existing commensal microbiota. The microbiota recipients were co-housed with microbiota donors of the same genotype for 4 weeks, during this period the donors continued to be exposed to cigarette smoking. All mice were sacrificed after being cohoused for 4 weeks, and fecal samples were frozen down at the time of collection. DNA was isolated using Qiagen QIAmp DNA Stool Kit, according to the kit protocol. Total DNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. 14 PCR amplicons, representing all 9 16S variable regions, were constructed using the Fluidigm Access Array System. 5ng/ul of DNA were input into each reaction. The sample inlets consisted of 1X High Fidelity FastStart Reaction Buffer without MgCl2 (Roche), 4.5nM MgCl2 (Roche), 5% DMSO (Roche), 200uM PCR Grade Nucleotide Mix (Roche), 0.05 U/μL 5 U/μL FastStart High Fidelity Enzyme Blend (Roche), 1X Access Array Loading Reagent (Fluidigm), 1ul DNA, and water. The primers were added to the assay inlets at 200nM forward and reverse primers with 1X Access Array Loading Reagent. The samples were harvested after PCR amplification was performed on the BioMark HD system from Fluidigm. Each sample was harvested and indexed using unique 10 base pair sequences with 14 rounds of PCR to incorporate each index sequence. All samples were pooled into 48 sample libraries and cleaned using bead purification.
characteristics.characteristic: description
characteristics.text: non-smoking, co-housed with smoking mice
characteristics.characteristic: environmental history
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: host organism
characteristics.text: mouse gut metagenome
characteristics.characteristic: organism
characteristics.text: mouse gut metagenome
characteristics.characteristic: organism
characteristics.text: feces
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCIT_C13234
characteristics.characteristic: organism part
characteristics.text: mouse gut metagenome
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: 12480
characteristics.characteristic: title