characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-04-06T17:03:25Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-05-16T18:32:19Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104030551
characteristics.characteristic: External Id
characteristics.text: unspecified
characteristics.characteristic: INSDC center name
characteristics.text: 2018-04-06T17:03:25Z
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: ERS1694444
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5707:9450
characteristics.characteristic: Submitter Id
characteristics.text: 10 to 12
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common 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. Four- to six-week-old mice were exposed to mainstream cigarette smoking 4 cigarettes/day, 5 days/week, for 6 weeks, using Kentucky research cigarette 3R4F in a smoking chamber. All mice were sacrificed after completing 6 weeks of smoking exposure, and full thickness ileum were stored in RNAlater for RNA extraction. RNA was isolated using Qiagen RNeasy Minikit, according to the kit protocol. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. Total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 4ng/ul. Library preparation was performed by the Genome Technology Access Center (GTAC) at Washington University. Library preparation was performed with 1ug of total RNA. Total RNA integrity was determined using an Agilent bioanalyzer. Ribosomal RNA was removed by a hybridization method using Ribo-Zero kits (Illumina-EpiCentre). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 using single reads extending 50 bases.
characteristics.characteristic: description
characteristics.text: non-smoking
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.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: small intestine
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002108
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: 9450
characteristics.characteristic: title