Supporting Information
Figure S1  Number of Overlapping and Non-Overlapping Transcriptionally Enriched Genes in NP and hESC between Pairwise Gene-Level Comparisons of Different hESC to NP Samples Displayed as Venn Diagrams
For each hESC to NP pair, the percentage of enriched genes found in the intersection was indicated in parentheses.
(174 KB PDF) Click here for additional data file.   Table S1  Number of Probesets with Significant “Outliers”
(39 KB DOC) Click here for additional data file.   Table S2  REAP[+] Exons Were Defined as Probesets Matching Internal Exons with at Least Two (or Three) Significant Points
“1” in the table indicated that the event had to be present in the comparisons above (Cyt-ES versus hCNS-SCns; HUES6-ES versus hCNS-SCns; Cyt-NP versus Cyt-ES; HUES6-NP versus HUES6-ES).
(44 KB DOC) Click here for additional data file.   Table S3  Experimental Validation of REAP[+] Targets
“N” and “P” indicated negative or positive validation by RT-PCR. The genomic coordinates of the exon for hg17 were represented as chromosome, followed by start and end, separated by “:”. “1” and “−1” indicated whether the exon was REAP[+] “1” or REAP[−] “−1”, at the different cutoffs of one to four.
(130 KB DOC) Click here for additional data file.   Table S4  Conserved 5-mers Enriched in Downstream/Upstream Intronic Regions of REAP[+] Exons Included in ES (NP) and Skipped in NP (ES)
For example, in row 6 ACCTG was enriched in the downstream intronic regions of exons included in ES and skipped in NP, relative to REAP[−] exons.
(34 KB DOC) Click here for additional data file.