Table 2.
Antibodies and Other Reagents
| Antibodies and Reagents | Manufacturer |
|---|---|
| Antibodies for flow cytometry | |
| anti-mouse CD45-PE-Cy7(103114) | BioLegend |
| anti-mouse Ly6G-FITC (127605) | BioLegend |
| anti-mouse CD11c-PerCP-Cy5.5(117327) | BioLegend |
| anti-mouse CD3-APC (300311) | BioLegend |
| anti-mouse NK1.1-PE (108707) | BioLegend |
| anti-mouse CD19-APC-Cy7(115529) | BioLegend |
| anti-mouse CD11b-PE (101207) | BioLegend |
| anti-mouse CD68-APC-Cy7(137023) | BioLegend |
| anti-mouse CCR7-APC (120108) | BioLegend |
| anti-mouse Ly6C-APC (128016) | BioLegend |
| anti-mouse F4/80-APC (123116) | BioLegend |
| anti-human CD45-PE-Cy7(368532) | BioLegend |
| anti-human CD66b-FITC (305104) | BioLegend |
| anti-human CD11c-PerCP-Cy5.5(301624) | BioLegend |
| anti-human CD11b-PE (301306) | BioLegend |
| anti-human CD68-APC-Cy7(333822) | BioLegend |
| anti-human CCR7-APC (353214) | BioLegend |
| anti-mouse CD4-PerCP-Cy5.5(100433) | BioLegend |
| anti-mouse IFN-γ-APC (505810) | BioLegend |
| anti-mouse CCR7-Brilliant Violet 605 (120125) | BioLegend |
| anti-mouse CD163-Brilliant Violet 421 (155309) | BioLegend |
| anti-mouse CD206-Alexa Fluor 647 (141711) | BioLegend |
| anti-mouse MHC II Brilliant Violet 510 (107635) | BioLegend |
| anti-mouse IL-12-APC (505205) | BioLegend |
| anti-mouse IL-10-Brilliant Violet 421 (505021) | BioLegend |
| Antibodies for immunohistochemical staining | |
| rabbit anti-human/mouse Rev-erbα(ab174309, 1:100) | Abcam |
| horseradish peroxidase anti-rabbit IgG (ZB-2301) | Zhongshan Biotechnology |
| sheep anti-mouse Reg3b (AF5110) | R&D Systems |
| horseradish peroxidase anti-sheep IgG (ZB-2306) | Zhongshan Biotechnology |
| rabbit anti-mouse β-defensin-1(PA5-75666) | Thermo Fisher Scientific |
| Antibodies for immunofluorescence | |
| rabbit anti-human/mouse Rev-erbα(ab174309;ab251057, 1:100) | Abcam |
| mouse anti-human/mouse CD326 (EpCAM) (ab212580, 1:100) | Abcam |
| rabbit anti-human CCL21(ab231116;ab248260, 1:100) | Abcam |
| rabbit anti-human/mouse pepsinogen II (ab259997, 1:100) | Abcam |
| rabbit anti-mouse CD11b (ab232427, 1:100) | Abcam |
| rat anti-mouse Ly6C (ab15627, 1:100) | Abcam |
| mouse anti-H pylori (188-10881-1, 1:100) | RayBiotech |
| goat anti-rabbit-TRITC (ZF-0316, 1:50) | Zhongshan Biotechnology |
| goat anti-rabbit-FITC (ZF-0311, 1:50) | Zhongshan Biotechnology |
| goat anti-mouse-TRITC (ZF-0313, 1:50) | Zhongshan Biotechnology |
| goat anti-mouse-FITC (ZF-0312, 1:50) | Zhongshan Biotechnology |
| goat anti-rat-FITC (ZF-0315, 1:50) | Zhongshan Biotechnology |
| Antibodies for neutralizing and blocking | |
| anti-human CCL21 (Goat IgG) (AF366) | R&D Systems |
| Goat IgG Control (AB-108-C) | R&D Systems |
| anti-human CCR7 (Mouse IgG2a) (MAB197) | R&D Systems |
| Mouse IgG2a Isotype Control (MAB003) | R&D Systems |
| anti-mouse CCL21 (Rat IgG2a) (MAB457) | R&D Systems |
| anti-mouse CCR7 (Rat IgG2a) (MAB3477) | R&D Systems |
| Rat IgG2a Isotype Control (MAB006) | R&D Systems |
| anti-mouse Reg3b (MAB5110) | R&D Systems |
| anti-mouse β-defensin-1(PA5-75666) | Thermo Fisher Scientific |
| Antibodies for Western blot | |
| rabbit anti-human/mouse Rev-erbα(ab174309, 1:1000) | Abcam |
| rabbit anti-human ERK1/2(4695, 1:1000) rabbit anti-human ERK1/2(ab218017, 1:1000) | Cell Signaling Technology Abcam |
| rabbit anti-human p-ERK1/2(4370S, 1:2000) | Cell Signaling Technology |
| rabbit anti-human p-ERK1/2(ab242418, 1:2000) | Abcam |
| rabbit anti-human/mouse GAPDH (BL042F, 1:1000) | Beijing Ray Antibody Biotech |
| rabbit anti-human/mouse GAPDH (ab186930;ab199554, 1:1000) | Abcam |
| rabbit anti-human/mouse Lamin B1(ab133741;ab220797, 1:1000) | Abcam |
| rabbit anti-cagA(sc-28368, 1:100) | Santa Cruz Biotechnology |
| ELISA kits | |
| mouse Reg3b (ml058487-C) | ML Bio |
| mouse β-defensin-1(ml002270-C) | ML Bio |
| human CCL21(ELH-6Ckine-1) | RayBiotech |
| mouse CCL21(ELM-6Ckine) | RayBiotech |
| mouse IFN-γ(1210002) | Dakewe Biotech Co |
| Reagents for signaling pathways inhibition | |
| MEK-1 and MEK-2 inhibitor U0126(U120) | Merk Millipore |
| MAPK inhibitor SB203580(S8307) | Calbiochem |
| JNK inhibitor SP600125(S5567) | Calbiochem |
| STAT3 phosphorylation inhibitor FLLL32(406111) | MedKoo Biosciences |
| JAK inhibitor AG490(200121) | Merk Millipore |
| PI3K-AKT inhibitor Wortmannin (406447) | Merk Millipore |
| Reagents for Luciferase Reporter Assay | |
| Dual-luciferase reporter assay system (E1910) | Promega |
| Endo-free Plasmid Mini Kit (D6950) | Omega |
| Pierce Magnetic CHIP Kit (26157) | Thermo Fisher Scientific |
| truChIP Chromatin Shearing Kit (520127) | Covaris |
| 16% Formaldehyde, Methanol-Free (12606) | Cell Signaling Technology |
| Antibodies for CHIP | |
| Rev-erbα rabbit mAb (13418s, 1:100) | Cell Signaling Technology |
| NF-κB p65 rabbit mAb (8242s, 1:100) | Cell Signaling Technology |
| SimpleChip human NR1D1 promoter primers (13413s) | Cell Signaling Technology |
| Purified anti-CD3 antibodies (100201) | BioLegend |
| Purified anti-CD28 antibodies (102101) | BioLegend |
| Human CD326 microbeads (130-061-101) | Miltenyi Biotec |
| Mouse CD326 microbeads (130-105-958) | Miltenyi Biotec |
| EasySep Mouse CD4+ T Cell Isolation Kit (19852) | StemCell Technologies |
| Dynabeads FlowComp Mouse CD4 Kit | Invitrogen |
| 5-μm pore size Transwells (3421) | Corning |
| 0.4-μm pore size Transwells (3413) | Corning |
| Collagenase IV (17104019) | Gibco |
| DNase I (AMPD1) | Sigma-Aldrich |
| Phorbol myristate acetate (P8139) | Sigma-Aldrich |
| Ionomycin (407951) | Sigma-Aldrich |
| Golgistop (554724) | BD Pharmingen |
| Perm/Wash solution (554714) | BD Pharmingen |
| Carboxylfluorescein succinimidyl ester (CFSE) (65-0850-84) | eBioscience |
| Rev-erbα agonist SR9009(554726) | Merck |
| Rev-erbα antagonist SR8278(554718) | Merck |
| Cremophor (61791-12-6) | BASF |
| DMSO (D2650) | Sigma-Aldrich |
| Protein Extraction Reagent (89901) | Pierce |
| SuperSignal West Dura Extended Duration Substrate kit (34075) | Thermo |
| Fetal bovine serum (FBS) (10091148) | Gibco |
| Fetal bovine serum (FBS) (10099141C) | Invitrogen |
| Penicillin/Streptomycin (15140122) | Gibco |
| RPMI-1640(SH30809.01) | Hyclone |
| DMEM/F12 (1:1) (SH30023.01) | Hyclone |
| Ficoll-Paque Plus (17-1440-02) | GE Healthcare |
| lyses solution (RT122) | TIANGEN |
| TRIzol reagent (15596026) | Invitrogen |
| Lipofectamine 2000 Transfection Reagent (11668027) | Invitrogen |
| Lipofectamine RNAiMAX Transfection Reagent (13778150) | Invitrogen |
| QIAamp DNA Mini Kit (51304) | QIAGEN |
| PrimeScript RT reagent Kit (R037A) | TaKaRa |
| Real-time PCR Master Mix (QPK-201) | Toyobo |
| pGL3-basic vector (E1751) | Promega |
| Recombinant mouse Reg3b (5110-RG) | R&D Systems |
| Recombinant mouse β-defensin-1(228-11913-1) | RayBiotech |
| Recombinant mouse CCL21(457-6C) | R&D Systems |
| Recombinant human CCL21(366-6C) | R&D Systems |
| All other recombinant human/mouse cytokines and chemokines | PeproTech |
APC, allophycocyanin; APC-Cy7, allophycocyanin-cyanin 7; ChIP, chromatin immunoprecipitation; FITC, fluorescein isothiocyanate; IFN, interferon; PE, phycoerythrin; PE-Cy7, phycoerythrin-cyanin 7; PerCP-Cy5.5, peridin chlorophyl protein-cyanin 5.5.