Feb 07, 2024
Spatially variable gene detection
- 1University of Oxford
Protocol Citation: Peter Kilfeather 2024. Spatially variable gene detection. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzxp28gx1/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: 94802
Funders Acknowledgement:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
Spatially variable gene detection from Kilfeather, Khoo et al., 2024
Protocol
Protocol
Spatially variable genes were identified using SpatialDE2 with default settings. Coordinates and full expression matrices of each brain were supplied, divided by cell type. To combine results from separate samples, a meta-analysis was performed on the raw P values from each sample, using Fisher’s method. The Benjamini & Hochberg correction for multiple comparisons was subsequently used and genes were considered spatially variable with an adjusted P value of < 0.01.