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Chapter 4 Outputs

dataset
posted on 2023-04-19, 09:19 authored by Holly Whitfield

This item contains two transcriptomic signatures that I derived for Chapter 4 of my thesis using publicly available single-cell RNA-seq data from a mouse gastrulation atlas (E-MAT-6967) and neural crest cells during delamination (GSE129114). I processed cells from both datasets separately and performed pseudobulk differential expression analyses to derive two signatures of developmental epithelial-mesenchymal transition (EMT) programs. Despite the abundance of EMT signatures in the literature and the interest in developmental EMTs by the EMT research community, there are no developmentally-derived EMT signatures to my knowledge.

For the first signature, I used primitive streak and mesodermal cells from the gastrulation atlas to obtain a transcriptomic signature of primitive streak epithelial-mesenchymal transition (EMT). 

For the second signature, I derived a signature of neural crest cell EMT during delamination that reflects their migration from the neural tube. For reasons that are described in my thesis, I performed 4 different statistical contrasts to compare neural tube and migratory cells then took the union of genes across the 4 analyses. The NCC signature provided only includes genes that were upregulated in migratory NCC populations.

The excel file contains the differential expression output for all analyses and the gmt file contains the signatures as a GeneSetCollection object. The signatures can be loaded into R using GSEABase::getGmt() for further analyses.  

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