SAMN39986722
External Id
Technical University of Munich
INSDC center name
2025-03-01T00:51:28.893Z
INSDC first public
2025-03-01T00:51:28.893Z
INSDC last update
SRS20560374
INSDC secondary accession
live
INSDC status
MISAG.miscellaneous
NCBI submission model
MISAG.miscellaneous.6.0
NCBI submission package
SRS20560374
SRA accession
2022-02-21
collection_date
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.
description
NA
env_broad_scale
NA
env_local_scale
NA
env_medium
NA
geo_loc_name
H. pylori infected, eradicated and reinfected mice
isolate
NA
isolation_source
NA
lat_lon
Mus musculus
http://purl.obolibrary.org/obo/NCBITaxon_10090
organism
C57BL/6
strain
Single cell RNA sequencing of CD3+ T cells from female C57BL/6 mice
title