SRX5583962 Lgr5_Hp_4 SRP189651 bp0 For the RNAseq analysis, we infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group). A slice of stomach tissue was used for CFU analysis as described above to confirm successful colonization. The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 M mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. For RNA sequencing, we prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system. Our Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT. Bulk-sorted cell libraries were sequenced on the Illumina NextSeq 500 in a single high-output, dual-indexed, paired-end run producing 75 base pair length reads. SRS4545498 Lgr5_Hp_4 Lgr5_Hp_4 RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX5583963 Lgr5_Hp_6 SRP189651 bp0 For the RNAseq analysis, we infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group). A slice of stomach tissue was used for CFU analysis as described above to confirm successful colonization. The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 M mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. For RNA sequencing, we prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system. Our Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT. Bulk-sorted cell libraries were sequenced on the Illumina NextSeq 500 in a single high-output, dual-indexed, paired-end run producing 75 base pair length reads. SRS4545499 Lgr5_Hp_6 Lgr5_Hp_6 RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX5583964 Lgr5_NI_1 SRP189651 bp0 For the RNAseq analysis, we infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group). A slice of stomach tissue was used for CFU analysis as described above to confirm successful colonization. The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 M mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. For RNA sequencing, we prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system. Our Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT. Bulk-sorted cell libraries were sequenced on the Illumina NextSeq 500 in a single high-output, dual-indexed, paired-end run producing 75 base pair length reads. SRS4545500 Lgr5_NI_1 Lgr5_NI_1 RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX5583965 Lgr5_NI_3 SRP189651 bp0 For the RNAseq analysis, we infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group). A slice of stomach tissue was used for CFU analysis as described above to confirm successful colonization. The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 M mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. For RNA sequencing, we prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system. Our Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT. Bulk-sorted cell libraries were sequenced on the Illumina NextSeq 500 in a single high-output, dual-indexed, paired-end run producing 75 base pair length reads. SRS4545501 Lgr5_NI_3 Lgr5_NI_3 RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX5583966 Lgr5_NI_5 SRP189651 bp0 For the RNAseq analysis, we infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group). A slice of stomach tissue was used for CFU analysis as described above to confirm successful colonization. The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 M mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. For RNA sequencing, we prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system. Our Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT. Bulk-sorted cell libraries were sequenced on the Illumina NextSeq 500 in a single high-output, dual-indexed, paired-end run producing 75 base pair length reads. SRS4545502 Lgr5_NI_5 Lgr5_NI_5 RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500 SRX5583967 Lgr5_Hp_2 SRP189651 bp0 For the RNAseq analysis, we infected Lgr5eGFP mice with H. pylori for 2 months and used uninfected littermates as controls (n = 3 mice per group). A slice of stomach tissue was used for CFU analysis as described above to confirm successful colonization. The stomach was opened along the lesser curvature, washed with saline solution and the antrum with transitional zone isolated. The antrum was incubated for 2 h in a buffered saline solution containing 10 mM EDTA, then washed in the buffered saline solution and vigorously shaken to isolate individual gastric glands. Isolated gastric glands were visualized by DIC microscopy and then resuspended in TrypleExpress (Gibco) and Accumax cell dissociation solution (Innovative Cell Technologies). After incubation at 37 C for 15 minutes, serum was added to inactivate the dissociation enzymes, and after another incubation period of 30 minutes, cells were collected by centrifugation, resuspended in medium containing 10% FBS and filtered through a 40 M mesh. Cells were analyzed for eGFP expression by flow cytometry (BD FACSAria II Flow Cytometer). Live cells were gated for negative DAPI staining. Single viable epithelial cells were gated by forward scatter and pulse-width parameters. For RNA sequencing, we prepared cDNA from H. pylori-infected mice and uninfected control samples in triplicate using a Nugen Ovation V2 RNA-seq system. Our Illumina library construction used the Epicentre (Illumina) Nextera DNA Sample Prep kit combined with Illumina-compatible adaptors and PCR primers from IDT. Bulk-sorted cell libraries were sequenced on the Illumina NextSeq 500 in a single high-output, dual-indexed, paired-end run producing 75 base pair length reads. SRS4545503 Lgr5_Hp_2 Lgr5_Hp_2 RNA-Seq TRANSCRIPTOMIC cDNA NextSeq 500