GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE347nnn/GSE347271/primaryOK200TranscriptomicsHomo sapiens Chlorocebus sabaeusExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE347271GEOGSEfalseSingle-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cellsMicrosporidia are single-celled, obligate intracellular parasites closely related to fungi. One of the most common human-infecting microsporidian species, Encephalitozoon intestinalis, is an enteric parasite that invades and replicates within the epithelial lining of the small intestine. Two epithelial cell lines, Caco-2 and Vero cells, are routinely used as in vitro models of E. intestinalis infection. Knowledge of host transcriptional responses at the single-cell level, as well as parasite development in these host cell lines would be a valuable resource for understanding host-pathogen interactions. Here, we use scRNA-seq to investigate the host response to E. intestinalis infection and the transcriptional dynamics of parasite development in both Caco-2 and Vero cell lines. We observe that most host cells have no direct transcriptional response to parasite invasion or intracellular replication, suggesting that cells fail to detect and/or fail to respond to direct E. intestinalis infection, consistent with previous single-cell transcriptomics of E. intestinalis-infected macrophages. Our data suggest that a small subset of host cells detect intracellular parasites late in the life cycle, and signal to neighboring cells, leading to broad activation of a TNF-ɑ response. Analysis of parasite transcripts reveals a developmental program that correlates with the morphological stages of the parasite life cycle. Together our data provide insights into a shared host transcriptional response to E. intestinalis infection, and the datasets presented are a valuable resource for future studies Microsporidia are single-celled, obligate intracellular parasites closely related to fungi.2026/09/17GSE347271GSM10049101GSM10049100GSM10049099GSM100490983703034281347271Homo sapiens Chlorocebus sabaeus