Feb 07, 2024
Stereo-seq cell type abundance analysis
- 1University of Oxford
Protocol Citation: Peter Kilfeather 2024. Stereo-seq cell type abundance analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn3kjzl5d/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 07, 2024
Last Modified: February 07, 2024
Protocol Integer ID: 94803
Keywords: seq cell type abundance analysis stereo, seq cell type abundance analysis, seq cell type abundance analysis from kilfeather, cell, seq
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
Stereo-seq cell type abundance analysis from Kilfeather, Khoo et al., 2024
Protocol
To test for differential abundance of cell types between age groups, we used mixed effects modelling of associations of single cells (MASC). MASC tests whether cell type membership of individual cells is influenced by an experimental covariate of interest, while accounting for technical covariates and biological variation. We specified mouse genotype as a fixed covariate and mouse of origin as a random effect in the generalized, mixed-effect model. Changes in cell type abundance were considered significant at FDR-P < 0.01.