Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain

Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain. Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3’ gene expression kit, version 3.1) and processed according to the manufacturer’s protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R.