Journal: Cells

Article Title: scRNA-Seq of Cultured Human Amniotic Fluid from Fetuses with Spina Bifida Reveals the Origin and Heterogeneity of the Cellular Content

doi: 10.3390/cells12121577

Figure Lengend Snippet: Identification of fetal/maternal origin of the cell types detected in the cultured AF samples of this study. ( A ) Violin plot showing the expression of the male-specific gene RPS4Y1 per cluster in the merged analysis of the five AF samples included in the scRNA-seq analysis (two from male and three from female fetuses). The gene was expressed in all clusters, indicating that all detected cell types were of fetal origin (data from AF samples from four fetuses with spina bifida aperta (SBA) and one from a healthy fetus). ( B – F ) Violin plots showing the expression levels of RPS4Y1 per cluster in each of the five AF samples included in the scRNA-seq analysis. The gene was expressed in all clusters in the AF samples from the two male fetuses (m) but was absent in all clusters in the AF samples from the three female fetuses (f), indicating that all detected clusters (and therefore cell types) were of fetal origin. The cell clusters are shown in different colors and the legend indicates the assigned cell type.

Article Snippet: For single-cell transcriptomics analysis of cultured AF cells, the droplet-based 10X Genomics Chromium scRNA-seq platform was used [ ] at the Functional Genomics Center Zurich (University of Zurich, Zurich, Switzerland).

Techniques: Cell Culture, Expressing

Journal: Cells

Article Title: scRNA-Seq of Cultured Human Amniotic Fluid from Fetuses with Spina Bifida Reveals the Origin and Heterogeneity of the Cellular Content

doi: 10.3390/cells12121577

Figure Lengend Snippet: Neural-associated marker expression in one normal AF and in four AF from fetuses with neural tube defects. ( A ) Heatmap with the expression pattern of neural-cell-lineage markers and selected neuron- and neuroglia-associated markers in the 13 clusters and in each of the five AF samples that were subjected to scRNA-seq. The Z score indicates relative expression. ( B ) t-SNE plots of all single cells with the expression of representative neural-cell-lineage-specific marker genes. SOX2 and NES for neural progenitors, GAP43 for neurons and MAP2 for glial cells. Black dashed lines mark the neural clusters of interest. ( C ) Dot plot highlighting the expression of the neural-associated genes from ( A ) in each of the five AF samples included in the scRNA-seq analysis (one AF sample from a normal fetus and four from fetuses with SBA). ( D ) Weighted mean expression score of the neural-cell-lineage marker set from ( A ) in the one normal versus the four SBA samples. The score was computed by the package decoupleR .

Article Snippet: For single-cell transcriptomics analysis of cultured AF cells, the droplet-based 10X Genomics Chromium scRNA-seq platform was used [ ] at the Functional Genomics Center Zurich (University of Zurich, Zurich, Switzerland).

Techniques: Marker, Expressing