Feb 07, 2024
Differential gene expression analysis
- 1University of Oxford
Protocol Citation: Peter Kilfeather 2024. Differential gene expression analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.5jyl8p7k9g2w/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: 94804
Funders Acknowledgement:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
Differential gene expression analysis from Kilfeather, Khoo et al., 2024
Protocol
Protocol
Differential gene expression analysis in TRAP samples (including calculation of gene enrichment and depletion, relative to tissue homogenate RNA) was performed using DESeq2 (v1.36.0, RRID:SCR_015687) in R (v4.2.1, RRID:SCR_001905) with Bioconductor (v3.15, RRID:SCR_006442). Adaptive shrinkage of log fold change estimates was performed using ashr. The following settings were changed from defaults: minReplicatesForReplace = Inf, cooksCutoff = Inf, filterFun = ihw, lfcThreshold = log2(1.05). Genes were classed as significantly differentially expressed with an FDR-adjust P value < 0.01. Protein-protein interactions were obtained using STRINGdb (version 11) with a minimum confidence threshold of 0.4.