Hi colleagues. I am very new to single cell sequencing and IPA analyses, but I have a background in R and Python programming. In a previous study from my research group, it was identified that two types of cells in mice interacted with each other only when they were co-cultured with direct contact under certain conditions. I have a set of differentially expressed genes from the single cell sequencing data of one of those cells cultured alone under three conditions including the control condition. I made use of this tutorial tutorial https://satijalab.org/seurat/pbmc3k_tutorial.html . My next task is to discover by IPA analyses, which of the differentially expressed genes are located on the cell surface (or is a surface marker). I am not so clear about how I can proceed and I will be very grateful for any help hints on the directions I can take.
Thank you all in advance for your contributions.
I perform surface analysis using the gene list from ”da Cunha JP, Galante PA, de Souza JE, de Souza RF, Carvalho PM, Ohara DT, et al. Bioinformatics construction of the human cell surfaceome. Proc Natl Acad Sci U S A. 2009;106:16752–16757. https://doi.org/10.1073/pnas. 0907939106.“
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