Single-cell RNA-seq of undirected human cerebral organoids (HuCOs) infected with MV1 or MV2 compared with uninfected controls at 120 and 180 days post-infection

Undirected human cerebral organoids (HuCOs) derived from induced pluripotent stem cells (hiPSCs) were used to model neural development and infection response in vitro. Organoids were maintained in spinning bioreactors and divided into three experimental groups: MV1-infected, MV2-infected, and uninfected control (NBH). Each infection group was harvested at two developmental stages, approximately 120 and 180 days post-infection (dpi), following five months of infection. Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 and sequenced on an Illumina NovaSeq 6000 platform. The study aimed to characterize infection-induced transcriptional and cellular changes across time points and between infection subtypes. This dataset provides a high-resolution single-cell transcriptomic resource to explore cellular heterogeneity and host–pathogen interactions in undirected human cerebral organoids. Overall design: Human cerebral organoids (HuCOs) derived from hiPSCs were generated under undirected differentiation conditions and maintained in spinning bioreactors. Organoids were assigned to three experimental groups: MV1-infected, MV2-infected, and uninfected control (NBH). Samples were collected at two time points, 120 and 180 days post-infection (dpi), yielding a total of 16 single-cell RNA-seq libraries (8 per time point). Single-cell suspensions were prepared from each organoid and processed with the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1. Libraries were sequenced on an Illumina NovaSeq 6000 to generate paired-end reads. Data were processed with Cell Ranger v7.1 (10x Genomics) using the GRCh38 reference genome and analyzed with the Loupe Browser for clustering and differential expression. Comparative analyses included: (1) NBH vs MV1 vs MV2 at 120 dpi; (2) NBH vs MV1 vs MV2 at 180 dpi; (3) 120 vs 180 dpi within NBH, MV1, and MV2 groups.