Data files and codes used in the reanalysis of the mouse encode comparative gene expression data

<p>We provide supplementary files of the python codes used to process and prepare the data for analysis with R, and the data files for the python codes. We also provide the R codes we used to perform the different analyses as supplementary files, as well as the input for the R codes. Please see supplementary text files for more details.</p

Standard DE genes identified between species for given cell classifications.

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Comparative skeletal cell culture model.

Schematic of the differentiation protocol and the stages at which single-cell RNA-seq data were collected (A), along with descriptions of the human and chimpanzee cell lines used (B), a diagram of the overall study design (C), and cell images from one human cell line and one chimpanzee cell line at each stage of differentiation (D). Pluripotent cells (Time 0) and mesenchymal cells (Time 1) are phase contrast images at 4X magnification, and osteogenic cells (Time 2) are stained with Alizarin Red and zoomed out to display the entire cell culture well. Silhouette images were adapted from http://phylopic.org/ and courtesy of T. Michael Keesey and Tony Hisgett (http://creativecommons.org/licenses/by/3.0/).</p

Gene Set Enrichments in Standard Interspecific DE Genes.

Enrichment of external DE gene sets among standard interspecific DE genes (FDR (TIF)</p

Details and results of the Oil Red O analyses.

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Data QC in General Ad Hoc Assignment Cell Annotations.

(A) UMAP dimensional reduction plot of scRNA-seq data with cells labeled by their ad hoc assignment. (B) Bar plot depicting the number of chimpanzee and human cells in each ad hoc assignment. (C) Violin plots displaying the distribution of UMI counts per cell for each ad hoc assignment. (D) Violin plots displaying the distribution of gene counts per cell for each ad hoc assignment. (E) The correlation of average gene expression patterns between technical replicates (human and chimpanzee) collected in each ad hoc assignment. (F-H) Enrichment of GO functional categories in marker genes for iPSC.c1 (F), MSC.c1 (G), and Osteogenic.c1 (H). The top 5 GO functions identified in biological processes (BP), cell components (CC), and molecular functions (MF) are displayed along with the adjusted p-value (p-adjust), the number of marker genes overlapping a GO function (Count), and the ratio of overlapping to non-overlapping marker genes for a given GO function (Gene Ratio). (TIF)</p

Data QC in General Unsupervised Cluster Cell Annotations.

(A) UMAP dimensional reduction plot of scRNA-seq data with cells labeled by their assigned unsupervised cluster (resolution = 0.05). (B) Bar plot depicting the number of chimpanzee and human cells assigned to each cluster. (C) Violin plots displaying the distribution of UMI counts per cell for each cluster. (D) Violin plots displaying the distribution of gene counts per cell for each cluster. (E) The correlation of average gene expression patterns between technical replicates (human and chimpanzee) collected in each cluster. (F-H) Enrichment of GO functional categories in marker genes for iPSC.c1 (F), MSC.c1 (G), and Osteogenic.c1 (H). The top 5 GO functions identified in biological processes (BP), cell components (CC), and molecular functions (MF) are displayed along with the adjusted p-value (p-adjust), the number of marker genes overlapping a GO function (Count), and the ratio of overlapping to non-overlapping marker genes for a given GO function (Gene Ratio). (TIF)</p

Data Integration, Reproducibility, and Candidate Gene Expression.

(A) UMAP dimensional reduction plots of scRNA-seq data with cells labeled by the stage of differentiation at which they were collected and separated by species. (B) The correlation of average gene expression patterns between technical replicates separated by species. Plots from left to right: (1) correlation in pluripotent cells (Time 0), (2) correlation in mesenchymal cells (Time 1), (3) correlation in osteogenic cells (Time 2). (C) Dot plots depicting the scaled average expression (dot color intensity) and the proportion of cells expressing each gene (dot size) of candidate genes (x-axis) at each stage of differentiation (y-axis). (TIF)</p

Significant enrichment of GO functional categories in the top 100 genes defining gene programs identified in the topic modeling analyses.

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Cell culture details for all samples used in the study.

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