title: Single cell RNA sequencing of CD3+ T cells from female C57BL/6 mice
organism: Mus musculus
description: Lymphocytes were isolated from the stomach of chronically infected, eradicated, and re-infected mice (H. pylori PMSS1 strain), and CD45+CD3+PI- cells were sorted using a FACSAria III flow (BD Biosciences). Afterwards, the single cells were encapsulated into droplets with the ChromiumTM Controller and processed following the manufacturers specifications (Chromium Next GEM Single Cell 3' Kit v3.1, 10X Genomics). Libraries were quantified with the Qubit 3.0 Fluorometer (Thermo Fisher Scientific), and quality control was performed on a 2100 Bioanalyzer with a High Sensitivity DNA kit (Agilent). For library sequencing, the NovaSeq 6000 platform was used. The sequencing data were annotated against the murine reference genome GRCm38 (mm10-2020-A) using CellRanger software (v.6.1.0). All subsequent analyses were performed using SCANPY V1.826. General preprocessing was performed according to good practice in RNA seq analysis by choosing under 15 percent mitochondrial genes and regressing out the cell cycle, mitochondrial genes, and total counts. Subsequently, the data was counted, normalized per cell, and transformed logarithmically.
attributes.tag: isolate
attributes.value: H. pylori infected, eradicated and reinfected mice
attributes.tag: collection_date
attributes.value: 2022-02-21
attributes.tag: env_broad_scale
attributes.value: NA
attributes.tag: env_local_scale
attributes.value: NA
attributes.tag: env_medium
attributes.value: NA
attributes.tag: geo_loc_name
attributes.value: NA
attributes.tag: isolation_source
attributes.value: NA
attributes.tag: lat_lon
attributes.value: NA
attributes.tag: strain
attributes.value: C57BL/6
attributes.tag: BioSampleModel
attributes.value: MISAG.miscellaneous