Information on genes tested in this study is provided in Supplementary Table 3. Previously described methods4 were used in Northern blotting, RT-PCR, and real-time RT-PCR analyses for AtPIP1 4 expression.
Interestingly, antiestrogens repress transcription of all ERα target genes tested in S phase.
Compared to wild type, the driver alone caused elevations in mRNA levels of the three structural genes tested, in addition to CF2 itself (data not shown).
Of the large number of candidate genes tested in this study, only FLNB was detected by both methods and across both populations in the iCP cleft category.
For both the up-regulated and down-regulated genes in an experimental set, we simulated random gene lists of the same size by drawing without replacement from the set of all genes tested in the experiment.
We also established that mRNA expression patterns appear to be fairly stable as mRNA expression of three SVSP genes tested in different cell lines remained largely constant over an observation period of up to 8 weeks.
rt-PCR confirmed the Affymetrix results for 7 of the 8 genes tested in 20 cases and 20 controls (FKBP8, ITPK1, MARCH2, PNPLA2, TUBA3, UBXD1, FTL); the remaining gene (PINK1) did not show a significantly different expression on rt-PCR.
By contrast, only 2 out of the 7 genes in cohort (ii) were significantly upregulated in p97 knock-down cells (Figure 4c), and none of the genes tested in cohort (iii) were induced by knock-down of p97 (Figure 4d).
None of the cholesterol metabolism related genes tested in our experiment met our filtering criterion of 1.5-fold change in two consecutive conditions (for example see Cyp51, Dhcr7, Lss, Nsdhl, Sc4 mol, Sqle; Fig. S4).
Interestingly, AcK9 signal was not reduced at any of the genes tested in the N-myc minus cells and in fact exhibited consistent increases with loss of N-myc at several genes.
For the non-Hox genes tested in blastocysts, levels of H4K8ac, H3K4me3 and H3K9me2 generally showed little change as a result of VPA treatment at the 8-cell to morula stage (Fig. 2).
