MicroRNA Profiling Reveals Unique miRNA Signatures in IGF-1 Treated Embryonic Striatal Stem Cell Fate Decisions in Striatal Neurogenesis In Vitro
Figure 5
(a) A Venn diagram displayed the common and differentially expressed miRNAs in control and treated striatal stem cells. The profiling had revealed a distinct set of 26 common candidates among both group D and group E derived ESSCs. (b) Partek Genomics Suite based analysis of miRNA profiles. The genome analysis software imports affymetrix-CEL files for each data set.Assignments of sample attributes or the Categorical attributes:These attributes are imposed to the imported data sets () as per their specification such as treated, untreated, and nature. Assignment of sample attributes was displayed in three different rows. PCA analysis for sample variation: Principal components 1, 2, and 3 in 3D space represented approximately 49.7% of the variation in the scatter plot. Three main clusters were observed among the differentiating cells, including: (1) Embryonic striatal stem cells, ESSCs without any growth factor (red), (2) ESSCs from treatment group D (blue), and (3) ESSCs from treatment group E (green). Validation of sample clusters. The histogram represents the visualization of data distribution or the variation in the data analysis by the Partek software. Three samples showed similar frequency, revealing no discrepancy among these three samples, prior to sample analysis. Sources of variation between samples: Sources of variation or error were predicted for data using all test variables in the ANOVA model. The variation bar chart showed “signal-to-noise ratio” or “F ratio” in the y-axis. The “mean F-ratio” was the mean signal to noise ratios for all computed variables for the factors in x-axis. Spatial patterning of miRNA distribution: The representative volcano plots displayed spatial patterning of miRNA distribution for different groups on the basis of their P values and fold regulation. Each volcano plot is also shown along with corresponding heat maps indicating the list of candidates detected in both control versus treatment groups. (c) Fourteen differentially expressed miRNAs were detected in group D striatal stem cells. Out of these, twelve were found to be upregulated and two were downregulated. For the group E, six differentially expressed miRNAs were detected where three of the miRNAs were found to be up regulated while another three were down regulated. Among all these miRNAs, ESSC-specific candidates were selected on the basis of significant differential expression. IGF-1-derived ESSCs (group D) demonstrated significant upregulation of miR-143, miR-433 and downregulation of miR-503. ESSCs from group E (LIF/IGF-1 combinatorial effect) displayed upregulation of miR-181, miR-326 and downregulation of miR-22.
