An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation

An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation

IntroductionRNA sequencing (RNA-seq) can measure whole transcriptome gene expression from tissues or even individual cells, providing a powerful tool to study the immune response. Analysis of RNA-seq data involves mapping relatively short sequence reads to a reference genome, and quantifying genes b...

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Main Authors: Sebastian Benjamin, GW McElfresh, Maanasa Kaza, Gregory J. Boggy, Benjamin Varco-Merth, Sohita Ojha, Shana Feltham, William Goodwin, Candice Nkoy, Derick Duell, Andrea Selseth, Tyler Bennett, Aaron Barber-Axthelm, Nicole N. Haese, Helen Wu, Courtney Waytashek, Carla Boyle, Jeremy V. Smedley, Caralyn S. Labriola, Michael K. Axthelm, R. Keith Reeves, Daniel N. Streblow, Jonah B. Sacha, Afam A. Okoye, Scott G. Hansen, Louis J. Picker, Benjamin N. Bimber
Format: Article
Language:English
Published: Frontiers Media S.A. 2025-08-01
Series:Frontiers in Immunology
Subjects:
single-cell RNA-seq (scRNA-seq)
T cells
bioinformatics
immunogenetics
major histocompatability complex (MHC)
Online Access:https://www.frontiersin.org/articles/10.3389/fimmu.2025.1596760/full
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https://www.frontiersin.org/articles/10.3389/fimmu.2025.1596760/full

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