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

ABSTRACT: Understanding lung immunity requires an unbiased profiling of tissue-resident T cells at their precise anatomical locations within the lung, but such information has not been characterized in the immunized mouse model. In this pilot study, using 10x Genomics Chromium and Visium platform, we performed an integrative analysis of spatial transcriptome with single-cell RNA-seq and single-cell ATAC-seq on lung cells from mice after immunization using a well-established Klebsiella pneumoniae infection model. We built an optimized deconvolution pipeline to accurately decipher specific cell-type compositions by anatomic location. We discovered that combining scATAC-seq and scRNA-seq data may provide more robust cell-type identification, especially for lineage-specific T helper cells. Combin

SUBMITTER: Xu Z 

PROVIDER: S-EPMC9418911 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature