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.