Single nucleus RNA sequencing of hippocampal tissue from wildtype and SHIP1 conditional knockout mice at postnatal day 15.

This study corresponds to the single nucleus RNA sequencing (snRNAseq) analysis done as part of the manuscript "Microglial SHIP1 controls synaptic pruning in the developing hippocampus via the complement system" by Matera et al. INPP5D, which encodes the lipid phosphatase SHIP1, is one of the most common genes associated with the risk of Alzheimer's disease and is enriched in microglia in the central nervous system. SHIP1 has been found to be highly expressed in plaque-associated microglia. However, how it regulates microglial function and influences brain physiology has been poorly investigated. In this study, we generated a snRNAseq dataset from the hippocampi of wildtype (WT) and conditional SHIP1 knockout (KO) mice at postnatal day 15. By predicting cell-cell communication, we found decreased neuronal interactions in KO mice, in line with results of synaptic loss in the rest of the manuscript. Overall design: Wildtype (WT) and conditional SHIP1 knockout (KO) mice were used in this study. KO mice were Inpp5d-floxed under a Cx3cr1 Cre-promoter. Recombination was induced by tamoxifen injection at postnatal days 3 and 4. Fresh frozen hippocampal tissues from one hemisphere were dissected from WT (n=4) and KO (n=4) mice at postnatal day 15. We used 2 male and 2 female pups per group. After performing single nucleus isolation, we enriched for lesser abundant cell types using a FANS strategy after staining for NeuN and Olig2. Nuclei were then loaded on 10x Genomics Chromium single cell chips. cDNA libraries were prepared and dual indexed using the 10x Genomics Chromium Single Cell 3' Reagents kit. Samples were then pooled in equimolar ratios and sequenced on a NextSeq2000 platform. Data were pre-processed with CellRanger7, and then analyzed using Seurat v4.3.