Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Large-Scale Protein Assay Identifies Novel Protein Biomarkers Associated With Arterial Stiffness and Vascular Calcification Measures.

International journal of hypertension·2026
Same author

A cross-sectional study of oxidative stress pathway genotypes and their interactions with environmental pollutant levels identifies associations with gene expression and lung function.

EBioMedicine·2026
Same author

Improving crystal material property prediction with multi-view geometric graph transformer.

Nature communications·2026
Same author

Heterogeneous causal mediation analysis using Bayesian additive regression trees.

Biometrics·2026
Same author

Multivalent nanobodies for potent and broad neutralization of Staphylococcus aureus toxins.

Nature communications·2026
Same author

An assessment of measurement error when using maternal urinary phthalates as proxies for placental tissue levels in the estimation of the association of prenatal phthalates and infant anogenital distance.

Journal of exposure science & environmental epidemiology·2026

Related Experiment Video

Updated: Aug 30, 2025

Isolation of Live Myeloid and Epithelial Cell Populations from the Mouse Lung
06:02

Isolation of Live Myeloid and Epithelial Cell Populations from the Mouse Lung

Published on: January 31, 2025

855

Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs

Zhongli Xu1,2, Xinjun Wang3, Li Fan4

  • 1Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.

Iscience
|August 30, 2022
PubMed
Summary

This study maps immune cells in the mouse lung after immunization. It reveals how T helper cell locations and related signals change, offering new insights into lung immunity mechanisms.

Keywords:
Biological sciencesImmunologyOmicsTranscriptomics

More Related Videos

Characterization of Immune Cells and Proinflammatory Mediators in the Pulmonary Environment
09:00

Characterization of Immune Cells and Proinflammatory Mediators in the Pulmonary Environment

Published on: June 24, 2020

3.4K
Flow Cytometric Analysis for Identification of the Innate and Adaptive Immune Cells of Murine Lung
09:57

Flow Cytometric Analysis for Identification of the Innate and Adaptive Immune Cells of Murine Lung

Published on: November 16, 2021

6.9K

Related Experiment Videos

Last Updated: Aug 30, 2025

Isolation of Live Myeloid and Epithelial Cell Populations from the Mouse Lung
06:02

Isolation of Live Myeloid and Epithelial Cell Populations from the Mouse Lung

Published on: January 31, 2025

855
Characterization of Immune Cells and Proinflammatory Mediators in the Pulmonary Environment
09:00

Characterization of Immune Cells and Proinflammatory Mediators in the Pulmonary Environment

Published on: June 24, 2020

3.4K
Flow Cytometric Analysis for Identification of the Innate and Adaptive Immune Cells of Murine Lung
09:57

Flow Cytometric Analysis for Identification of the Innate and Adaptive Immune Cells of Murine Lung

Published on: November 16, 2021

6.9K

Area of Science:

  • Immunology
  • Genomics
  • Computational Biology

Background:

  • Understanding lung immunity necessitates precise anatomical profiling of tissue-resident T cells.
  • Such detailed spatial information has been lacking in immunized mouse models.
  • Current methods do not fully capture the spatial distribution of immune cells within the lung microenvironment.

Purpose of the Study:

  • To perform an unbiased, spatial profiling of lung immune cells in an immunized mouse model.
  • To investigate the anatomical locations and cell-type compositions of T cells within the lung.
  • To explore the potential of single-cell multi-omics for uncovering spatial-dependent mechanisms of lung immunity.

Main Methods:

  • Integrative analysis of spatial transcriptome (10x Visium) with single-cell RNA-seq and single-cell ATAC-seq.
  • Utilized the 10x Genomics Chromium and Visium platforms for high-resolution data acquisition.
  • Developed an optimized deconvolution pipeline for accurate cell-type identification by anatomical location.

Main Results:

  • Demonstrated that combining scATAC-seq and scRNA-seq enhances cell-type identification, particularly for T helper cells.
  • Observed dynamic changes in T helper cell locations and their associated chemokines using multi-modal single-cell analysis.
  • Successfully deciphered specific cell-type compositions based on anatomical location within the lung.

Conclusions:

  • Single-cell multi-omics analysis is a powerful approach for studying lung immunity.
  • This study provides a proof-of-principle for uncovering spatial and cell-type-dependent immune mechanisms.
  • The findings highlight the importance of anatomical context in understanding immune responses within the lung.