Chapter 4 Outputs

<p>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 (<a href="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6967" target="_blank">E-MAT-6967</a>) and neural crest cells during delamination (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129114" target="_blank">GSE129114</a>). 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.</p> <p>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). </p> <p>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.</p> <p>The excel file contains the differential expression output for all analyses and the gmt file contains the signatures as a <a href="https://rdrr.io/bioc/GSEABase/man/GeneSetCollection-class.html" target="_blank">GeneSetCollection </a>object. The signatures can be loaded into R using GSEABase::getGmt() for further analyses.  </p>