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

doi:10.3389/fimmu.2025.1596760

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Community

Back to search

Article

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

Frontiers in immunology - 1 Jan 2025

Benjamin Sebastian, McElfresh G W, Kaza Maanasa, Boggy Gregory J, Varco-Merth Benjamin, Ojha Sohita, Feltham Shana, Goodwin William, Nkoy Candice, Duell Derick, Selseth Andrea, Bennett Tyler, Barber-Axthelm Aaron, Haese Nicole N, Wu Helen, Waytashek Courtney, Boyle Carla, Smedley Jeremy V, Labriola Caralyn S, Axthelm Michael K, Reeves R Keith, Streblow Daniel N, Sacha Jonah B, Okoye Afam A, Hansen Scott G, Picker Louis J, Bimber Benjamin N

Abstract excerpt

Introduction: RNA 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 based on the position of alignments relative to annotated genes. While this is usually robust, genetic polymorphism...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Gene Expression Profiling

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Share to Histocompatibility Antigens Class I

Share to Mycobacterium tuberculosis

Share to RNA-Seq

Share to Sequence Analysis, RNA

Share to Single-Cell Analysis

Share to Single-Cell Gene Expression Analysis

Share to Transcriptome

Source

Open in PubMed Open full text

Identifiers

PMID: 40861433
DOI: 10.3389/fimmu.2025.1596760
PMCID: PMC12370678

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 11 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation.PMID 40861433Read ↗

Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomesSemantic proximity Read ↗

Single‐Cell Sequencing Reveals Functional Alterations in TuberculosisSemantic proximity Read ↗

A comprehensive workflow for allele-specific immune gene quantification and expression analysis in single-cell RNA-seq dataSemantic proximity Read ↗

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytesSemantic proximity Read ↗

Reference-free multiplexed single-cell sequencing identifies genetic modifiers of the human immune responseSemantic proximity Read ↗

Detecting T cell receptor rearrangements <i>in silico</i> from non-targeted DNA-sequencing (WGS/WES)Semantic proximity Read ↗

FB5P-seq: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cellsSemantic proximity Read ↗

Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissuesSemantic proximity Read ↗

ITRAP2, a flexible and robust strategy to assign antigen recognition of T-cells in coupled single-cell TCR-pMHC assaySemantic proximity Read ↗

scHLAcount: Allele-specific HLA expression from single-cell gene expression dataSemantic proximity Read ↗

Recovery of Paired T Cell Receptors from Single-cell Seq-Well LibrariesSemantic proximity Read ↗

Profiling immunoglobulin repertoires across multiple human tissues by RNA SequencingSemantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.