Here, the user has the option of using his/her own list of probes corresponding to Y chromosome genes or using the probe lists included with the package.
Quantitative real time Taqman gene expression analysis was performed according to the manufacturer's instructions using the probe sets listed in Table S2 and processed as described [63].
Allelic states of substitution and small insertion/deletion polymorphisms in the human and in the great apes samples were determined by dynamic ASO hybridization as described [ Bourgeois and Labuda, 2004], using the ASO probes listed in Supplementary Table S2.
cDNA was diluted to 100 ng/μL for subsequent TaqMan quantitative PCR analysis (ABI 7500) using the probes and primers listed in Table 2.
We queried the DNase I hypersensitivity of genomic segments as devised elsewhere [24], using oligonucleotides probes listed in supplementary Table S1.
Seven groups of duplex real-time PCR simultaneous amplifications were optimized using the iCycler (Bio-Rad, Hercules, CA,) and the FAM, HEX two channel method using the primers and probes listed in Table 1.
Biotin-labeled double-stranded oligonucleotides were used as probes listed below: wild-type NF-κB consensus binding sequence: 5′-agttgag gggactttcccaggc-3′ [ 34]; wild-type Mcl-1-κB binding sequence: 5′-ggagtc ggggtcttccccagtttt-3′, corresponding to the nucleotides of the human Mcl-1 promoter.
Ferret-specific ISH probes were cloned using the primers listed in Supplementary Table S2.
We tested the ability of YY1, SOX9, abaA, SEF4, VDR and GRLF consensus sequences to out-compete the binding to the −41bp C-allele and A-allele probes, using the competitor oligonucleotides listed in Supplementary Table S1.
Two distinct CYP19 genomic areas and three distinct areas covering the CYP19 PII region were amplified using the primers and BlackBerry-quenched hydrolysis probes listed in Table 2. Amplification was performed in a 20 μl reaction solution using the LC480 Probes Master (Roche) reaction mix, 0.5 μM of each primer, 0.125 μM of each hydrolysis probe and 2 μl gDNA as template.
