DOI: 10.17044/scilifelab.22778920.v1
title: Spatial Multimodal Analysis (SMA) - Spatial Transcriptomics

description: This dataset contains Spatial Transcriptomics (ST) data matching with Matrix Assisted Laser Desorption/Ionization - Mass Spetrometry Imaging (MALDI-MSI). This data is complementary to data contained in the same project. FIles with the same identifiers in the two datasets originated from the very same tissue section and can be combined in a multimodal ST-MSI object. For more information about the dataset please see our manuscript posted on BioRxiv (doi: https://doi.org/10.1101/2023.01.26.525195). 
This dataset includes ST data from 19 tissue sections, including human post-mortem and mouse samples. The spatial transcriptomics data was generated using the Visium protocol (10x Genomics). The murine tissue sections come from three different mice unilaterally injected with 6-OHDA. 6-OHDA is a neurotoxin that when injected in the brain can selectively destroy dopaminergic neurons. We used this mouse model to show the applicability of the technology that we developed, named Spatial Multimodal Analysis (SMA). Using our technology on these mouse brain tissue sections we were able to detect both dopamine with MALDI-MSI and the corresponding gene expression with ST. This dataset includes also one human post-mortem striatum sample that was placed on one Visium slide across the four capture areas. This sample was analyzed with a different ST protocol named RRST (Mirzazadeh, R., Andrusivova, Z., Larsson, L. <em>et al.</em> Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. <em>Nat Commun</em> <strong>14</strong>, 509 (2023). https://doi.org/10.1038/s41467-023-36071-5), where probes capturing the whole transcriptome are first hybridized in the tissue section and then spatially detected.
Each tissue section contained in the dataset has been given a unique identifier that is composed of the Visium array ID and capture area ID of the Visium slide that the tissue section was placed on. This unique identifier is included in the file names of all the files relative to the same tissue section, including the MALDI-MSI files published in the other dataset included in this project. In this dataset you will find the following files for each tissue section:
- raw files: these are the read one fastq files (containing the pattern *<strong>R1*fastq.gz</strong> in the file name), read two fastq files (containing the pattern *<strong>R1*fastq.gz</strong>  in the file name) and the raw microscope images (containing the pattern <strong>*Spot*.jpg</strong> in the file name). These are the only files needed to run the Space Ranger pipeline, which is freely available for any user (please see the 10x Genomics website for information on how to install and run Space Ranger);
- processed data files: we provide processed data files of two types:
 a) Space Ranger outputs that were used to produce the figures in our publication;
 b) manual annotation tables in csv format produced using Loupe Browser 6 (csv tables with file names ending <strong>_RegionLoupe.csv</strong>, <strong>_filter.csv</strong>, <strong>_dopamine.csv</strong>, <strong>_lesion.csv</strong>, <strong>_region.csv</strong> patterns); 
 c) json files that we used as input for Space Ranger in the cases where the automatic tissue detection included in the pipeline failed to recognize the tissue or the fiducials.
 Using these processed files the user can reproduce the figures of our publication without having to restart from the raw data files.
The MALDI-MSI analyses preceding ST was performed with different matrices in different tissue section. We used 1) 9-aminoacridine (9-AA) for detection of metabolites in negative ionization mode, 2) 2,5-dihydroxybenzoic acid (DHB) for detection of metabolites in positive ionization mode, 3) 4-(anthracen-9-yl)-2-fluoro-1-ethylpyridin-1-ium iodide (FMP-10), which charge-tags molecules with phenolic hydroxyls and/or primary amines, including neurotransmitters. The information about which matrix was sprayed on the tissue sections and other information about the samples is included in the metadata table. We also used three types of control samples:
- standard Visium: samples processed with standard Visium (i.e. no matrix spraying, no MALDI-MSI, protocol as recommended by 10x Gemomics with no exeptions) 
- internal controls (iCTRL): samples not sprayed with any matrix, neither processed with MALDI-MSI, but located on the same Visium slide were other samples were processed with MALDI-MSI
- FMP-10-iCTRL: sample sprayed with FMP-10, and then processed as an iCTRL.
This and other information is provided in the metadata table.