Table 1.
Gene Ontology of differentially regulated genes.
Table 2.
Significant JASPAR motifs over and under represented within 1.5 kb upstream of TSS of Notch regulated genes.
Table 3.
Regulatory proteins are not transcriptionally regulated by Notch.
Table 4.
Notch regulated genes with a putative CSL Binding Site within 1.5 kb upstream of TSS.
Table 5.
Differentially regulated genes shown by Chip-ChIP to be bound by activated Notch responsive CSL.
Figure 1.
Most unique reads map within 1.5 kb of the transcriptional start site.
Uniquely-aligned sequences (reads) were counted within a given 1000 base window relative to genomic positions. A step size of 50 bases was used for window overlap. Poisson distribution [116] was then used to generate P-values for each 1000 base window and windows were filtered by these values to generate a list of peaks. Significant peaks were windows with P-value less than 10−12.
Figure 2.
ChIP-seq reads mapping near the TSS.
The Integrated Genome Browser was used to visualize the ChIPseq peaks from both the Notch On and Notch Off sample. (a) TSS of the Myc gene. (b) TSS of the Hey1 gene (c) Hes1 gene and (d) Mns1 gene.
Figure 3.
Number of genes with at least one significant peak within 10 kb of the TSS.
Venn diagram shows the overlap between the three types of significant peaks detected within 10 kb of the TSS of annotated genes. The overlap regions represent genes with more than one type of peak within 10 kb of their TSS. 1) On only peak is when there is a significant peak in the Notch On sample but not in the Notch Off sample 2) Off only peak is when there is a peak in the Notch Off sample but not in the Notch On sample 3) Both peak is when there is a peak in both the Notch On and Notch Off Sample. Red is “on” and green is control. CBS is defined as CSL Binding Site.
Table 6.
Gene Ontology analysis of genes with at least one On only peak sorted by P-value.
Table 7.
List of pathways sorted by number of Gene Ontology analysis of genes with at least one On only peak sort by number of genes.
Table 8.
Differentially regulated genes shown by ChIP-seq to be bound by activated Notch responsive CSL.
Figure 4.
MicroRNA differentially regulated from Day 5 to Day 8.
Dendrogram showing a) the 83 differentially regulated microRNAs from day 5 to day 8. b) microRNAs that were differentially regulated comparing Day 8 Notch ON to Notch OFF and c) the microRNAs used for real-time PCR analysis. Data analyses were performed by using DNA-Chip Analyzer 1.3 [117]. The thresholds for selecting significant genes were set at a relative difference of >1.5-fold, an absolute difference of >100 signal intensity, and P<0.05.
Figure 5.
Seven MicroRNA expression on day 5, 6, 7 and 8.
Seven mature microRNAs including a) four downregulated and b) three upregulated that whose expression was analyzed using Taqman miRNA expression assay on day 5,6,7 and 8. The expression of the miRNA was normalized against the expression level of the control miRNA snoRNA202 (AF357327) and presented as the mean normalized expression.
Table 9.
miRNAs differentially regulated by overexpression of ligand independent Notch1.
Table 10.
miRNA differentially regulated during normal hematopoiesis and affected by the overexpression of activated Notch.
Table 11.
Timecourse of miRNA expression from Day 5 to Day 8 and the effect of overexpression of activated Notch.