SRP356121 PRJNA799312 GSE194142 AM in vivo and ex vivo RNAseq Here we show that alveolar macrophages maintain their core AM transcriptomic identity through culture expansion but show adaptations during culture expansion that are transient, reversible and fully restored upon transplantation into the alveolar niche. Overall design: For expanded AMs (exAM), total RNA was extracted from exAMs after 2 months of culture. exAM were transplanted into 2 months old CD45.1 mice and analyzed 4 months post transplantation. In vivo AM subsets were sorted (Live, Singlets, SiglecF+, CD11c+, CD45.2+ or CD45.1+) from total lung homogenates directly into RNA lysis buffer (RLT buffer, Qiagen) for RNA extraction. RNA-seq samples were generated from a pool of 3 mice or exAM cultures in duplicates. GSE194142 pubmed 35210623 parent_bioproject PRJNA799301