(accession nos.GSE108097andGSE134355). The mouse scATAC-seq dataset was generated by Cusanovich et al.63(accession no. GSE111586,https://atlas.gs.washington.edu/mouse-atac/data) and Di Bella et al.64(accession no.GSE153164), and the human scATAC-seq dataset by Domcke et al.65(...
Direct comparison of multiple scRNA-seq datasets generated by different scientific groups is often not possible due to batch effects. To circumvent this, multiple scRNA-seq data analysis and integration40,41,42,43approaches have been proposed. This also enabled the creation of so-called ‘integrated...
To validate these observations, we performed fluorescent immunohistochemistry in the adult mouse hippocampus with either a CYFIP1 or CYFIP2 antibody combined with antibodies for various cell-type-specific markers. Consistent with our analysis of the scRNAseq database, CYFIP1 signals were detected in...
transcriptomes in mouse and human atherosclerosis.Methods and results We integrated 12 scRNA-seq datasets of immune cells isolated from healthy or atherosclerotic mouse aortas, and scRNA-seq data from 11 patients (n=4 coronary vessels, n=7 carotid endarterectomy specimens) from two independent studies...
Initial assessment of scRNA-seq data on microglia from male and female mouse brains after permanent stroke We then asked two questions: how does permanent stroke impact the cellular heterogeneity of microglia, and do microglia respond to stroke differently in male vs female? To address these questio...
Raw sequencing data has been deposited at deposited at Gene Expression Omnibus (GEO) database (accession:GSE136441, ID: 200136441;https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136441). All original code has been deposited at GitHub (https://github.com/wanbaoniu8314/scRNAseq_mouse-...
The ideal strategy to overcome the limitations inherent in studying the highly heterogeneous brain is to use high-throughput methodology with the ability to capture spatial information, namely single-cell RNA-seq (scRNA-seq) and/or spatial transcriptomics. In contrast to the bulk RNA-seq methods us...
2c), as shown by a query of the Tabula muris, a single cell RNA sequencing (scRNA seq) database of cells from 20 different mouse organs37. RT-qPCR confirmed that tdTomato-tagged Plin2 was expressed in various organs of heterozygous tdTom-Plin2 mice (Fig. 2d). Imaging tdTom-PLIN2 ...
Source data are provided with this paper. All other data presented in this study are available from the corresponding authors upon request. Code availability The R code for scRNA-seq analysis can be found in the Supplementary Software. References Abdallah, M. W. et al. Amniotic fluid chemokines...
2.3. Single cell RNA-seq data analysis We preprocessed the scRNA-seq reads using the 10× GENOMICS Cell Ranger pipeline. In general, we aligned the reads to the mouse genome (mm10) with the setting “--r1-length=26 --r2-length=98.” We applied other default cell ranger parameters to ...