RNA sequencing of surface mucus producing cells captured with Laser Microdissection and Pressure Catapulting in mouse stomachs infected with Helicobacter pylori Sydney Strain 1
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.
RNAseq of foveolar cells from H. pylori infected mouse stomachs, with or without treatment with R-alpha-Methylhistamine
Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX)
Science for Life Laboratory (SciLifeLab)
National Microscopy Infrastructure (NMI)
Deciphering and reversing Helicobacter pylori infection induced impairments of the host mucin based defenses
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.
Specific diseases, disorders and medical conditions
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.
Bioinformatics and Computational Biology
Signs and symptoms; pathological conditions
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.
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.
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.
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.
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.
Histamine substituted in any position with one or more methyl groups. Many of these are agonists for the H1, H2, or both histamine receptors.
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.
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.
The viscous secretion of mucous membranes. It contains mucin, white blood cells, water, inorganic salts, and exfoliated cells.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
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).
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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
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.
Helicobacter pylori [H.pylori] as the cause of diseases classified to other chapters
laser microdissection and pressure catapulting (LMPC)