Table 1.
RNA-Seq Summary.
Figure 1.
Comparison of fold-changes (log2-transformed) of gene expression between iPSCs and day 10 neurons as measured by RNA-Seq (x-axis) and Affymetrix microarray (y-axis).
Table 2.
Gene Ontology (GO) terms for differentially expressed genes.
Figure 2.
Validation by RT-PCR and qPCR in unamplified RNAs.
Panel A, top band in each of the 4 sets is a beta-actin control; bottom band, specific transcripts. Lane 1, iPSCs; lane 2, day 14 neurons; lane 3, day 27 neurons; lanes 4 and 5, fetal brain (9 and 20 weeks, respectively); lanes 6 and 7, adult prefrontal cortex; lane 8, no RT (negative control). Panel B, same as A, but no 9 week fetal sample (lane 4 is 20 week fetal brain and lanes 5 and 6 are adult prefrontal cortex. Panel C, qPCR for MIAT and CRNDE in iPSCs (white bar) and day 14 neurons (black bar). Relative changes in gene expression were calculated using the 2−ΔΔCt method with β2-microglobulin (β2M) as a reference gene. Mean increase in transcripts in neurons was statistically significant (p<0.05). Error bar is SD based on 3 or 4 replicates, each done in triplicate.
Figure 3.
Splice variants in NRXN1 (panel A) and NRG1 (panel B).
Asterisk in A shows splicing across exons 19, 20 and 21 (exons 20 and 21 are only ∼2 kb apart and appear superimposed in figure). Asterisk in B covers exons 10 and 11 in the NRG1 isoform HRG-β2b. Panel C shows qPCR and relative changes in gene expression calculated using the 2−ΔΔCt method with β2-microglobulin (β2M) as a reference gene. Mean increase in transcripts in neurons was statistically significant (p<0.05). Error bar is SD based on 3 or 4 replicates, each done in triplicate.