RNA sequencing of surface mucus producing cells captured with Laser Microdissection and Pressure Catapulting in mouse stomachs infected with Helicobacter pylori Sydney Strain 1
type: Dataset
description: This RNA sequencing (RNAseq) data comes from mouse strain C57/BL6 gastric surface mucus cells, also known as foveolar cells. 5 mice were non-infected controls, 5 were infected with Helicobacter Pylori strain SS1 14 days prior to harvest, and another 5 were also infected with Helicobacter Pylori strain SS1 14 days prior to harvest, and furthermore these last 5 were also treated with R-alpha-Methylhistamine through oral gavage at 13, 10, and 7 days prior to harvest. 15 mice total. Surface mucous-producing epithelial cells were collected from the mice using laser microdissection and pressure catapulting (LMPC) with a PALM MicroBeam (Carl Zeiss, Oberkochen, Germany) at CCI (Centre for Cellular Imaging, Sahlgrenska Academy, Gothenburg, Sweden). Libraries were prepared with SMARTer Total Stranded RNA-seq, Pico input mammalian - V3 (Takara Bio, Kusatsu, Japan). The sample from one mouse in the infected/non-treated group failed library prep. The remaining 14 samples were sequenced with NovaSeq 6000 (Illumina, San Diego, USA at NGI (National Genomics Infrastructure, Solna, Sweden). The fastq-files were processed with the nf-core/rnaseq analysis pipeline, which was was run by NGI at UPPMAX (Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala, Sweden). The files follow the standard NGI distribution packaging, except for the folder structures 00-Reports/ and 01-RNA-Results/ which have been packaged as zip files for easier downloading.
alternate name: RNAseq of foveolar cells from H. pylori infected mouse stomachs, with or without treatment with R-alpha-Methylhistamine
conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
conditions of access: info:eu-repo/semantics/openAccess
contributor: Uppsala University
contributor: Science for Life Laboratory (SciLifeLab)
contributor: National Microscopy Infrastructure (NMI)
contributor: University of Gothenburg
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Mattias Erhardsson
creator: Sara Lindén
creator: Sinan Sharba
creator: Licínia Santos
date modified: 2026-02-23
date published: 2026-02-23
funding: Deciphering and reversing Helicobacter pylori infection induced impairments of the host mucin based defenses
  type: Grant
  funder: Swedish Research Council
language: English
is part of: https://doi.org/10.5878/28s1-7f49
keywords: Medication and treatment
keywords: Specific diseases, disorders and medical conditions
keywords: Bioinformatics (Computational Biology)
  type: DefinedTerm
  term code: 10203
keywords: Cell Biology
  type: DefinedTerm
  term code: 10604
keywords: Immunology
  type: DefinedTerm
  term code: 10605
keywords: Microbiology
  type: DefinedTerm
  term code: 10606
keywords: Bioinformatics and Computational Biology
  type: DefinedTerm
  description: Including: Modelling, Machine Learning
  term code: 10610
keywords: Signs and symptoms; pathological conditions
keywords: Public health
keywords: Molecular Biology
  type: DefinedTerm
  term code: 10616
keywords: Epithelial Cells
keywords: Gastric Mucins
keywords: Gastric Mucosa
keywords: Methylhistamines
keywords: Mice, Inbred C57BL
keywords: Mucins
keywords: Mucus
keywords: Gene Expression
keywords: Helicobacter pylori
keywords: Helicobacter Infections
keywords: Sequence Analysis, RNA
keywords: Gene Expression Profiling
keywords: Laser Capture Microdissection
keywords: Helicobacter pylori [H.pylori] as the cause of diseases classified to other chapters
keywords: laser microdissection and pressure catapulting (LMPC)
keywords: Foveolar cells
keywords: Gastric surface mucous cells
license: https://creativecommons.org/licenses/by/4.0/
publisher: University of Gothenburg
spatial coverage: Göteborg Municipality
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PropertyValue
property ID: DOI
value: 10.5878/ejy9-2895

Uppsala University
type: Organization
department: Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX)

Science for Life Laboratory (SciLifeLab)
type: Organization
department: National Genomics Infrastructure (NGI)

National Microscopy Infrastructure (NMI)
type: Organization
department: Centre for Cellular Imaging (CCI)

University of Gothenburg
type: Organization
department: Experimental Biomedicine (EBM)
department: Institute of Biomedicine
department: Institute for Biomedicine

Mattias Erhardsson
type: Person
affiliation: University of Gothenburg
family name: Erhardsson
given name: Mattias

Sara Lindén
type: Person
affiliation: University of Gothenburg
family name: Lindén
given name: Sara

Sinan Sharba
type: Person
affiliation: University of Gothenburg
family name: Sharba
given name: Sinan

Licínia Santos
type: Person
affiliation: University of Gothenburg
family name: Santos
given name: Licínia

Swedish Research Council
type: Organization

English
type: Language
alternate name: eng

Medication and treatment
type: DefinedTerm
description: Treatment of disease, or procedure/s of preventing it. Patient care at individual level. Research on medication and treatment of a disease. Data on, for instance, surgical procedures, rehabilitation, doctor consultation, physical therapy, musculoskeletal manipulations, care in hospital or home, psychotherapy, investigative techniques, medication.
term code: Health.MedicationAndTreatment

Specific diseases, disorders and medical conditions
type: DefinedTerm
description: Data on specific, diagnosed diseases, disorders or syndromes (often classified in ICD-10 or its earlier versions). For example, medical research on infectious diseases or the causes of diabetes, or data on the physical and mental recovery of people who have had heart surgery.
term code: Health.SpecificDiseasesDisordersAndMedicalConditions

Signs and symptoms; pathological conditions
type: DefinedTerm
description: Data on abnormal anatomical or physiological conditions, and objective or subjective manifestations of disease/symptoms, not classified as disease or syndrome (in which case 'Specific diseases, disorders or medical conditions' would be used). Includes clinical manifestations that can be objective when observed by a medical professional or subjective when perceived by the patient. E.g. pain, diarrhoea, rash, leg length inequality, insomnia, teeth grinding, inflammation, arrhythmia.
term code: Health.SignsAndSymptomsPathologicalConditions

Public health
type: DefinedTerm
description: Prevention and control of disease and disability, and the promotion of physical and mental health of the population on the international, national, state, or municipal level. For instance, health promotion, disease prevention, impact of public health programmes, managing local, national or global health issues, epidemiology of a disease, condition, or pathogen, or disease outbreak.
term code: Health.PublicHealth

Epithelial Cells
type: DefinedTerm
description: Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.
term code: D004847

Gastric Mucins
type: DefinedTerm
description: Mucins that are found on the surface of the gastric epithelium. They play a role in protecting the epithelial layer from mechanical and chemical damage.
term code: D005752

Gastric Mucosa
type: DefinedTerm
description: Lining of the STOMACH, consisting of an inner EPITHELIUM, a middle LAMINA PROPRIA, and an outer MUSCULARIS MUCOSAE. The surface cells produce MUCUS that protects the stomach from attack by digestive acid and enzymes. When the epithelium invaginates into the LAMINA PROPRIA at various region of the stomach (CARDIA; GASTRIC FUNDUS; and PYLORUS), different tubular gastric glands are formed. These glands consist of cells that secrete mucus, enzymes, HYDROCHLORIC ACID, or hormones.
term code: D005753

Methylhistamines
type: DefinedTerm
description: Histamine substituted in any position with one or more methyl groups. Many of these are agonists for the H1, H2, or both histamine receptors.
term code: D008761

Mice, Inbred C57BL
type: DefinedTerm
description: One of the first INBRED MOUSE STRAINS to be sequenced. This strain is commonly used as genetic background for transgenic mouse models. Refractory to many tumors, this strain is also preferred model for studying role of genetic variations in development of diseases.
term code: D008810

Mucins
type: DefinedTerm
description: High molecular weight mucoproteins that protect the surface of EPITHELIAL CELLS by providing a barrier to particulate matter and microorganisms. Membrane-anchored mucins may have additional roles concerned with protein interactions at the cell surface.
term code: D009077

Mucus
type: DefinedTerm
description: The viscous secretion of mucous membranes. It contains mucin, white blood cells, water, inorganic salts, and exfoliated cells.
term code: D009093

Gene Expression
type: DefinedTerm
description: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
term code: D015870

Helicobacter pylori
type: DefinedTerm
description: A spiral bacterium active as a human gastric pathogen. It is a gram-negative, urease-positive, curved or slightly spiral organism initially isolated in 1982 from patients with lesions of gastritis or peptic ulcers in Western Australia. Helicobacter pylori was originally classified in the genus CAMPYLOBACTER, but RNA sequencing, cellular fatty acid profiles, growth patterns, and other taxonomic characteristics indicate that the micro-organism should be included in the genus HELICOBACTER. It has been officially transferred to Helicobacter gen. nov. (see Int J Syst Bacteriol 1989 Oct;39(4):297-405).
term code: D016480

Helicobacter Infections
type: DefinedTerm
description: Infections with organisms of the genus HELICOBACTER, particularly, in humans, HELICOBACTER PYLORI. The clinical manifestations are focused in the stomach, usually the gastric mucosa and antrum, and the upper duodenum. This infection plays a major role in the pathogenesis of type B gastritis and peptic ulcer disease.
term code: D016481

Sequence Analysis, RNA
type: DefinedTerm
description: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
term code: D017423

Gene Expression Profiling
type: DefinedTerm
description: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
term code: D020869

Laser Capture Microdissection
type: DefinedTerm
description: Techniques using a laser to cut away and harvest a specific cell or cluster of cells from a tissue section while viewing it under the microscope.
term code: D061346

Helicobacter pylori [H.pylori] as the cause of diseases classified to other chapters
type: DefinedTerm
term code: B980

Göteborg Municipality
type: Place

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