Skip to main content
. Author manuscript; available in PMC: 2013 Aug 6.
Published in final edited form as: Stem Cells. 2012 Apr;30(4):741–752. doi: 10.1002/stem.1030

Figure 3. ChIP-seq and transcriptome analyses to identify N1ICD/RBPJ targets in vivo.

Figure 3

(A) A schema of experimental design: littermate wildtype and GFAP-Cre;N1ICD cortices were isolated and analyzed by RNA-seq and Affymetrix St 1.0 microarrays and ChIP-seq. (B) Numbers of differentially expressed genes measured by RNA-seq and Affymetrix microarray methods. (C) Numbers of genes within 15kb of significant peaks in wildtype and GFAP-Cre;N1ICD cortices. When the window is expanded to 50kb, a total of 8343 genes are associated with significant peaks in wildtype cortices. (D) Distribution of genomic regions bound by RBPJ. (E) Representative histogram presentations of aligned ChIP-seq reads in wildtype and transgenic cortices. Significant peaks are marked with bars below each histogram. Consensus RBPJ binding sites from earlier studies are marked with dots. (F) Independent ChIP validation of selected target sequences by realtime PCR. Untr6 and Untr17 are negative control regions. Also see Supplementary Figure 2.