DOI: 10.5061/dryad.cnp5hqcbq
title: A spatial atlas of the complement system uncovers unique expression patterns in postnatal brain development in mice

description: Recent studies have found non-immunological roles of the classical
 complement pathway (CP) in brain development and its involvement in
 neuropsychiatric and neurodegenerative diseases. However, multiple
 complement activation pathways exist beyond the CP, but their expression
 and function remain poorly understood in the brain. Using MERFISH, we
 constructed a comprehensive spatial transcriptomic atlas of the complement
 system in mouse brains from the late embryonic stage to adulthood. Here,
 we show that most complement genes are expressed locally with a remarkable
 degree of cellular, spatial, and temporal heterogeneity and that
 complement regulatory mechanisms are distinct from the periphery. Beyond
 confirming the known expression of the CP, our measurements reveal
 endogenous expression of the alternative pathway (AP), notably the AP
 activator Masp3 in immature brains. Masp3 deficiency causes working
 spatial memory defects and altered molecular structure of the brain,
 indicating a role of Masp3 in brain maturation, potentially via modulation
 of AP activity.
description: Spatial transcriptomic data were collected using MERFISH in p5
 and p60 wild-type mouse brain sagittal sections.
description: # A spatial atlas of the complement system uncovers unique expression
 patterns in postnatal brain development in mice
 [https://doi.org/10.5061/dryad.cnp5hqcbq](https://doi.org/10.5061/dryad.cnp5hqcbq) Decoded MERFISH molecule counts files and Python code used in the study 'A spatial atlas of the complement system uncovers unique expression patterns in postnatal brain development in mice' are uploaded here. ## Description of the data and file structure The following files are uploaded: 1\) geneNames.csv: names of gene targets included in the MERFISH experiment 2\) MERFISH_probe_sequences.fasta: MERFISH probe sequence 3\) .py files: Python code used to analyze these data 4\) 5 zip files correspond to MERFISH experiments with wild-type E18.5 (E18.5.zip), p5 (p5.zip), p60 (p60.zip) and 4-month-old (4mo.zip) mouse brains, and p5-Masp3 mice (Masp3-p5.zip). Each zip file contains the following raw data files:    * featureNames.csv files: unique feature names.  * feature_metadata.csv files: information of 'features', which is equivalent to a cell if the absolute volume is above the threshold. These files contain the following columns:  * feature_uID: unique identifier of each feature, corresponding to entries in featureNames.csv file * feature_ID: simple feature ID, numbered *  primary_fovID: field-of-view ID where the feature was located * abs_volume: absolute volume of the feature (um^3^) * centroid_1: feature spatial location, X-axis coordinate * centroid_2: feature spatial location, Y-axis coordinate * centroid_3: feature spatial location, Z-axis coordinate * boundaryX: cell segmentation boundary coordinate, X-axis  * boundaryY: cell segmentation boundary coordinate, X-axis * countsPerCell.csv files: RNA counts matrix, each column is an individual feature, each row corresponds to a target gene. The order of genes in these files is the same as in the geneNames.csv file. * countsPerCellCorrectedIn.csv: RNA inside of feature boundary, identified after error correction  * countsPerCellCorrectedOut.csv: RNA outside of feature boundary, identified after error correction  * countsPerCellExactIn.csv: RNA inside of feature boundary, identified without error  * countsPerCellExactOut.csv: RNA outside of feature boundary, identified without error  ## Sharing/Access information Link to data visualization platform: [moffittlab.github.io/visualization/2024_Complement_Brain](http://moffittlab.github.io/visualization/2024_Complement_Brain)