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Next hematopoietic cells were excluded by gating out CD45+ cells.
The CD8 immature single positive (ISP) and DP cell populations were isolated based on CD4, CD8 and TCRβ expression after gating out all cells staining with propidium iodide.
Cell acquisition was performed with FACSort Becton Dickinson in a region (R1) defined gating out only debris by forward and side scatter characteristics.
To identify the source of iNOS and CXCL11 in the gastric mucosa, macrophages (CD11b+Gr1−Siglec-F−MHC-II+), eosinophils (CD11b+Gr1−Siglec-F+MHC-II−) and the remaining cells after gating out macrophages and eosinophils (CD11b− and CD11b+Gr1+) were sorted from pooled gastric lamina propria cells of mice infected with H. pylori for 26 weeks (Fig. 4B).
For gene expression analysis, gastric macrophages (7AAD−, CD11b+, Gr1−, Siglec-F−, MHC-II+; 9×105 cells), eosinophils (7AAD−, CD11b+, Gr1−, Siglec-F+, MHC-II−; 6×105 cells), and the remaining cells after gating out macrophages and eosinophils (7AAD−, CD11b− and 7AAD−, CD11b+, Gr1+; 3×106 cells) were sorted to >92% purity.
Dead cells were excluded by gating out events with low FSC and SSC signals.
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Dead cells were gated out with Hoechst staining [12].
Dead cells were stained and gated out with 7-aminoactinomycin D (eBioscience).
Cell debris, cell clumps, dead cells and MEFs were gated out before sorting.
Cell debris was electronically gated out, based on forward light scatter.
As the stable cell lines were roughly 70% GFP positive, GFP negative cells were gated out in analysis.
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