H e fast staining kit

MALDI imaging data acquisition was performed with a mass detection range of m/z 400–2,200, 200 laser shots per spot, sampling rate of 1.25 GS/s, and raster width of 100 µm or 50 µm on a Rapiflex MALDI/TOF using flexControl 3.0 and flexImaging 3.0 (Bruker Daltonik). External calibration was performed using a peptide calibration standard (Bruker Daltonik). Spectra were processed using in flexAnalysis 3.0 (Bruker Daltonik).
Statistical data analysis was performed using SCiLS Lab software (Version2020a, SCiLS GmbH, Bremen, Germany). MALDI-IMS raw data were imported into the SCiLS Lab software and converted to the SCiLS Lab file format. Simultaneous preprocessing of all data sets was performed for better comparability of the sample sets. Imported data were preprocessed by convolution baseline removal (width: 20). Peak finding and alignment were performed using a standard pipeline with the following settings: ± 0.156 Da interval width, mean interval processing, and medium smoothing strength^{21 (link)–23 (link)}.
After MALDI imaging experiments, matrix was removed with 70% ethanol and tissue sections were stained with a hematoxylin/eosin (HE) fast staining kit (Roth, Germany).

Cryosections were stained with hematoxylin and eosin (HE). The staining was conducted using the H&E fast staining kit (Carl Roth, Karlsruhe, Germany). After washing in water for 10 s, the slides were incubated with the hematoxylin solution for 6 min. The slides were then rinsed in tap water and incubated in hydrochloric acid for 10 s. Blueing was conducted in tap water for 6 min. The slides were incubated in eosin for 1 min. The excess was washed off. For mounting, sections were dehydrated in 90% ethanol (Carl Roth, Karlsruhe, Germany) and absolute ethanol twice for 5 min. It was cleared in xylene twice for 5 min. Finally, cryosections were mounted in Eukitt (Sigma-Aldrich, St. Louis, MI, USA). Images were taken using the Eclipse Ti2 microscope (Nikon; Minato, Japan).

Skin, small intestine, and liver samples were collected from mice belonging to each experimental group, 3-weeks after transplant. Mouse skin biopsies were collected from the interscapular region of the mice. The small intestine samples were collected from the 2 cm region above the cecum, while the liver tissue was harvested from the left lobes. The samples were fixed for at least 48 h in 4% paraformaldehyde and embedded in paraffin. The sections were stained with hematoxylin and eosin (H & E fast staining kit, Carl Roth, Karlsruhe, Germany) according to manufacturer’s recommendation. The images were captured using a Leica DMi8 inverted microscope with a Leica DFC9000 sCMOS camera and processed using Leica LAS X software, version 3.3 (Leica Microsystems, Wetzlar, Germany).