Table 1.

Validation data for transcripts showing Nova-dependent changes in steady-state mRNA levels

DOI: http://dx.doi.org/10.7554/eLife.00178.006

qRT-PCR fold	Microarray-predicted fold	p-value	Gene
Transcripts with larger predicted fold changes
3.85 ± 0.84	3.39	<0.001	Dlg3 (Sap102)
3.79 ± 0.29	2.73	<0.001	Dzip1
2.40 ± 0.43	2.25	<0.001	Dtd1
3.64 ± 0.39	2.23	<0.001	Rasgrp2
2.42 ± 0.15	1.97	<0.001	Slc4a3
1.74 ± 0.28	1.81	<0.001	Slc4a10
2.06 ± 0.3	1.72	<0.001	Cacna2d3
1.73 ± 0.14	1.71	<0.001	Ahi1
1.90 ± 0.12	1.68	<0.001	Rasgrf1
1.83 ± 0.18	1.67	<0.001	Slc1a6
1.53 ± 0.13	1.67	<0.001	Lynx1
0.50 ± 0.07	0.68	<0.001	Cdk5rap2
0.40 ± 0.02	0.54	<0.001	Stx2(syntaxin 2)
0.30 ± 0.04	0.45	<0.001	Cpne3(copine III)
0.33 ± 0.07	0.34	<0.001	Scn9a
Transcripts with smaller predicted fold changes
1.98 ± 0.16	1.48	<0.001	Syt2
1.41 ± 0.1	1.47	<0.001	Actl6b
1.74 ± 0.07	1.40	<0.001	Gria3
1.56 ± 0.09	1.30	<0.001	Syngr3*
1.53 ± 0.13	1.29	<0.001	Glrb*
1.33 ± 0.20	1.25	<0.001	Gabbr1*
0.69 ± 0.07	0.77	<0.001	Plekha5

Summary of validation data for transcripts showing Nova-dependent change in steady-state mRNA levels. Upper table: validation data for transcripts showing larger fold predicted changes by microarray. Lower table: validation data for transcripts showing small predicted changes by microarray, to illustrate sensitivity of the data. In each table, the first column shows fold change from qRT-PCR, the second column shows fold change from Affymetrix-exon array data, the third column shows the p value and the fourth column shows the name of gene. Data for each gene is derived from three biologic replicates (three animals) and three technical replicates (nine reactions per point); these data are statistically significant (p<0.001; Student's t-test). Genes in bold are cryptic exons confirmed by sequencing (see Figure 3—source data 1 and Figure 4D). Genes with asterisk are those with robust 3′ UTR clusters (see Figure 8).