Il 10 mice

C57BL/6J wild type (WT) (fl/fl, cre-) and mice lacking PPARγ in T cells (PPARγ^fl/fl; CD4-Cre⁺) (32 (link)) or in myeloid cells (PPARγ^fl/fl; Lysozyme M Cre-) (33 (link)) were used in this study. CX₃CR1-GFP^+/+ reporter and IL-10^−/− mice were obtained from Jackson and bred in our mouse facilities for 6 months and 2 years, respectively. WT, CD4-cre and LysMcre mice used in these experiments originated from a colony kept for 10 years at Virginia Tech’s animal facilities. All mice used in these experiments were bred and maintained in the same colony. Mice were kept in the same room for breeding/maintenance under ABSL1 conditions and in a separate room under ABSL2 conditions for H. pylori challenge studies. For H. pylori infection, mice were challenged after a 6-hour fasting period with freshly prepared 5×10⁷ colony forming units (CFU) of strain SS1 given in sterile PBS through orogastric gavage on days 0 and 2. A non-infected group that received sterile PBS without any bacteria was included for each genotype.

Three week-old female C57BL/6 and IL-10^−/− mice were obtained from Jackson Laboratories (Bar Harbor, ME). Mice were group housed under a controlled temperature (25°C) and photoperiod (12:12-h light–dark cycle) and allowed unrestricted access to standard mouse chow diet and tap water. All studies were performed in accordance with the Institutional Animal Care and Use Committee at Georgia State University (Atlanta, GA). All procedures were approved and are registered in the protocol IACUC ID: A11025 (approval date from 8/30/2011 to 8/30/2014).

IL-10(−/−) mice, which develop spontaneous chronic intestinal inflammation due to T cell mediated aberrant immune response ^{7 (link); 8 (link)}, were obtained from Jackson Laboratory. Colonic mucosal VDR levels were examined at 3 months of age in wild-type and IL-10(−/−) mice. In other experiments, colitis was induced with 2,4,6-trinitrobenzene sulfonic acid (TNBS) in 8–12 week old C57BL/6 mice as previously described ^{9 (link); 6 (link)}. After overnight fasting mice were treated under anesthesia with 100 mg/kg TNBS (Sigma) dissolved in 50% alcohol via intrarectal injection using a 1-ml syringe fitted with an 18-gauge stainless steel gavage needle, with 50% alcohol treatment as control. The mice were killed at days 0, 1, 2 and 3 following TNBS treatment, and colonic mucosal levels of VDR protein, TNF-α and miR-346 transcripts were analyzed by Western blotting and real time RT-PCR. All animal studies were approved by the Institutional Animal Care and Use Committee at The University of Chicago.

Adult Albino Oxford strain rats were produced and maintained in the Baker Institute vivarium. ΔdblGATA (eosinophil-ablated), PHIL (eosinophil-ablated), VertX (IL-10 reporter), Rag1^−/−, IL-5-expressing transgenic (NJ.1638) (IL-5Tg⁺), IL-5Tg⁺ × MHCII^−/−, IL-5Tg⁺ × IL-4^−/− mice were bred at Cornell Transgenic Mouse Core Facility and offspring were transferred to the Baker Institute. IL-5Tg⁺ × IL-4^−/− and IL-5Tg⁺ × MHCII^−/− mice were generated by crossing and backcrossing on the deficient strains and genotype was confirmed by PCR. IL-10^−/− mice were purchased from The Jackson laboratory. Rag2^−/−γc^−/− (innate lymphoid cell-ablated) mice were purchased from Taconic. Arg1^flox/flox;Tie2cre (Arginase1 specifically ablated in myeloid cells) mice were a gift from Dr. Thomas Wynn (NIAID). PHIL mice were genotyped as described previously (23 (link)). All strains were on a C57BL/6 background. C57BL/6^NHsd mice were purchased from Taconic as wild type (WT) control. Animal care was in accordance with the guidelines of the Association for Assessment and Accreditation of Laboratory Animal Care and experiments were performed with the approval of the Institutional Animal Care and Use Committee of Cornell University.

Map3k14-flox mice (on C57BL/6 background), provided by Genentech, were generated using loxP system targeting exon 2 of the Map3k14 gene^{48 (link)}. The Map3k14-flox mice were crossed with Cd11c-Cre transgenic mice (B6 genetic background, Jackson Laboratories) to create Map3k14 DC-conditional KO or Map3k14-cKO (Map3k14^fl/flCd11c-Cre) and wild-type (Map3k14^+/+Cd11c-Cre) mice. Il10^−/− mice were purchased from Jackson Lab and crossed with Map3k14-cKO mice to produce Il10^−/−Map3k14-cKO and control Il10^−/− mice. Rorc^−/− and Tnfrsf1b^−/− mice were purchased from Jackson Lab. Nfkb2^lym1 mice were provided by R. Starr (Walter and Eliza Hall Institute of Medical Research)^{36 (link)}. Nfkb2^lym1/+ heterozygous mice were used in experiments since they display strong phenotype in impaired noncanonical NF-κB activation and function^{36 (link)}. All KO and conditional KO mice were crossed using heterozygous breeders to generate littermate KO and wild-type control mice for experiments. Mice were maintained in a specific pathogen-free facility, and all animal experiments were in accordance with protocols approved by the Institutional Animal Care and Use Committee of the University of Texas MD Anderson Cancer Center.