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Fig. 3 | Neural Development

Fig. 3

From: Postnatal developmental dynamics of cell type specification genes in Brn3a/Pou4f1 Retinal Ganglion Cells

Fig. 3

Candidate Brn3a target genes: Transcriptional and Translational regulators. RNASeq and ISH quantitation. In situ hybridization quantitation (a-c), and gene (aI- cI) and transcript (aII- cII) level RNASeq profiles for potential Brn3a target genes. a-c Box-whiskers plots for NBL and GCL of P0 and P3, and ONL, INL and GCL for P7-P22 retinas from Rax:Cre; Brn3aCKOAP/WT (left panel, WT) and Rax:Cre; Brn3aCKOAP/KO (right panel, KO) mice, harvested at P0, P3, P7, P14 and P22 show normalized (all except P0) mean intensity values from images of retinal sections (Y axis). Individual values for each layer are normalized to the respective IPL value in P3-P22 cases. X axis represents retinal layers: N – NBL, G – GCL, O – ONL, I – INL. Horizontal bars in panels denote observation pairs showing significant expression differences (Kolmogorov-Smirnov - KS2 test) between INL/NBL and GCL (black bar) and Brn3a-dependency by comparing respective WT and KO GCL values (green bar; significance levels * p < 0.05, ** p < 0.01, *** p < 0.001). All values and KS2 test outcomes are provided in Additional file 1: Table S1. aI-cI Gene level RNASeq profiles from affinity purified Brn3AP RGCs (RGC) and retinal supernatants (Retina) derived from P3 mice with the following genotypes: Pax6α:Cre; Brn3aCKOAP/WT (Brn3a-WT), Pax6α:Cre; Brn3aCKOAP/KO (Brn3a-KO), Pax6α:Cre; Brn3bCKOAP/WT (Brn3b-WT), and Pax6α:Cre; Brn3bCKOAP/KO (Brn3b-KO) (Sajgo et al. 2017). Values on the x axis are in CPM (counts per million reads), and bars represent mean values for two replicates (RGC samples) and single samples (retina supernatants). aII-cII Transcript level RNASeq profiles from the same samples as in aI-cI Values on the x axis are in FPKM, and bars represent mean values for two replicates (RGC samples) and single samples (retina supernatants). For each gene, only transcripts having detectable (> 1 FPKM values) in at least one of the samples are presented. The transcript (NM) number is indicated under the gene name. aI-aIII Rbfox1, bI-bIII Foxp2, cI-cII Tshz2

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