Evolution of primate gonadogenesis
Explore the single-nucleus RNA-seq and ATAC-seq data of the paper The evolution of gene regulatory programs controlling gonadal development in primates
Gene expression
This tab allows you to explore the single-nucleus gene expression data of human and marmoset developing ovaries and testes.
Select a category and gene to color the UMAPs accordingly. Clicking on a nucleus in the categorical UMAP (left) will highlight the corresponding category in the legend and subset the expression UMAP (right) to the nuclei of that category.
Human
Ovary
Testis
Marmoset
Ovary
Testis
Chromatin accessibility
This tab allows you to explore the single-nucleus chromatin accessibility data of human and marmoset developing ovaries and testes. Choose human or marmoset using the tabs below.
Peak table
This table shows all robust peaks and their associated metadata, including the genomic class, closest gene, predicted target genes (based on co-accessibility), sequence conservation, species group in which the associated sequence could be found, and the sex specificity of the peak accessibility in germ and supporting cells (some of these columns are only available for human data).
Click on a row to highlight the peak in the genome browser and show the peak accessibility and target gene expression UMAPs below.
Genome browser
After selecting a peak in the table above, the genomic region surrounding the peak will be shown in the genome browser. From here, you can group the normalized accessibility values (CPM) by different categories and navigate the browser.
Peak accessibility and target gene expression UMAPs
These UMAP embeddings show the nuclei of the snATAC-seq data colored by different categories (which you can switch using the drop-down menu), the normalized peak accessibility (CPM) and the imputed target gene expression of the peak selected in the table above.
The target genes were predicted based on co-accessibility, their expression was imputed by finding the most similar nuclei in the snRNA-seq data.
If there are more than one predicted target gene, you can switch the plotted gene using the drop-down menu.
Peak table
This table shows all robust peaks and their associated metadata, including the genomic class, closest gene, predicted target genes (based on co-accessibility), sequence conservation, species group in which the associated sequence could be found, and the sex specificity of the peak accessibility in germ and supporting cells (some of these columns are only available for human data).
Click on a row to highlight the peak in the genome browser and show the peak accessibility and target gene expression UMAPs below.
Genome browser
After selecting a peak in the table above, the genomic region surrounding the peak will be shown in the genome browser. From here, you can group the normalized accessibility values (CPM) by different categories and navigate the browser.
Peak accessibility and target gene expression UMAPs
These UMAP embeddings show the nuclei of the snATAC-seq data colored by different categories (which you can switch using the drop-down menu), the normalized peak accessibility (CPM) and the imputed target gene expression of the peak selected in the table above.
The target genes were predicted based on co-accessibility, their expression was imputed by finding the most similar nuclei in the snRNA-seq data.
If there are more than one predicted target gene, you can switch the plotted gene using the drop-down menu.
Human gene regulatory networks
This tab allows you to explore the gene regulatory networks of human germ and somatic cells in the developing ovary and testis.
You can select a gene and inspect its centrality in the networks of germ and somatic cell states. You can also visualize the up- and downstream interactions of the gene in the networks by selecting the cell type and the maximum degree of separation. The network plots are interactive, allowing you to hover over nodes to highlight their connections and move the nodes around to get a better overview.
Ovary
Testis
Cross-species gene expression trajectories
This tab allows you to explore gene expression trajectories along female and male germ cells and supporting cells across three species (human, marmoset, and mouse). The table below shows the classification of the trajectories as conserved or species-specific.
Select a gene from the dropdown menu below to visualize its expression trajectories in the different cell lineages. The expression data is binned along the pseudotime trajectory of each cell lineage. The stacked bar plots below show the distribution of cell subtypes across the pseudotime bins.
Female germ cells
Male germ cells
Female supporting cells
Male supporting cells
Trajectory assignments
This table shows the classification of gene expression trajectories into the following categories:
- conserved: trajectories that are conserved across all three species
- hum/mar/mou changed: trajectories that have a specific expression pattern in human/marmoset/mouse.
- undefined: trajectories that are sufficiently different in all three species (either due to lack of expression or a noisy pattern).
- no assignemt: genes that are not robustly expressed in at least two species.
Klinefelter syndrome
This tab allows you to explore the single-nucleus gene expression and chromatin accessibility data of the Klinefelter syndrome (XXY) dataset. The shown snRNA-seq and snATAC-seq UMAPs show co-embeddings of the 13 WPC XXY sample with the 12 WPC XY samples of the human testis atlas.
Gene expression
The first UMAP shows the snRNA-seq nuclei colored by karyotype (XY or XXY). The second UMAP shows the nuclei colored by cell type. Select a gene to show its expression in the third UMAP.
Chromatin accessibility
This table shows all robust peaks and their associated metadata, including the genomic class, closest gene, predicted target genes (based on co-accessibility), and sequence conservation.
Click on a row to highlight the peak in the genome browser and show the peak accessibility and target gene expression UMAPs below.
After selecting a peak in the table above, the genomic region surrounding the peak will be shown in the genome browser. From here, you can group the normalized accessibility values (CPM) by different categories and navigate the browser.
These UMAP embeddings show the nuclei of the snATAC-seq data colored by different categories (which you can switch using the drop-down menu), the normalized peak accessibility (CPM) and the imputed target gene expression of the peak selected in the table above.
The target genes were predicted based on co-accessibility, their expression was imputed by finding the most similar nuclei in the snRNA-seq data.
If there are more than one predicted target gene, you can switch the plotted gene using the drop-down menu.
Data and Information
This app allows you to explore the datasets of the paper Evolution of gene regulatory programs controlling gonadal development in primates (in preparation).
Contact: Nils Trost | Data Privacy Policy | Imprint