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Fig. 1. | BMC Biology

Fig. 1.

From: Notch signaling is a critical initiator of roof plate formation as revealed by the use of RNA profiling of the dorsal neural tube

Fig. 1.

Transcriptome analysis of small groups of premigratory NC and RP cells. a Principal component analysis shows a distinct segregation of transcripts for the purified populations of NC and RP cells along 2 principal components axes (PC1, PC2). b MA plot comparing RP over NC genes. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales. Genes upregulated in RP when compared to NC are above the red line and downregulated genes are below. c Heat map of 2171 differentially expressed genes (padj< 0.05) between NC and RP. Red and blue colors represent all significantly upregulated and downregulated genes, respectively. Normalized expression is shown after scaling the values for each gene. Genes and samples are ordered by hierarchical clustering, as indicated by the respective dendrograms. d, e Ingenuity pathway analysis (IPA) showing selected enriched categories in RP with reference to NC (red) or downregulated in RP/NC (blue), that include molecular functions and diseases (p value < 0.05). Categories with IPA Z-scores greater than 2 or smaller than − 2 can be considered to be significantly predicted to be up- (d, red) or down- (e, blue) regulated, respectively. fh Bromodeoxyuridine (BrdU) incorporation following a 1-h pulse at NC (E2, f) or RP (E3.5, g) stages. Note the presence of the BrdU+ nuclei (red) in NC domain but not in RP (delimited by dashed lines). Quantification of Brdu-positive cells (H) shows significantly reduced number of proliferating cells in the RP (*p < 0.001, N = 5/stage). i, j ISH for MycN shows downregulation in RP (delimited by dashed lines). Abbreviations, DRG, dorsal root ganglion, NT, neural tube. Bar = 50 μm

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