S1 nuclease mapping of transcripts (S1 analysis)
S1 analysis was performed as previously described (29), using 100 µg DNase I-digested total RNA (RNA isolation see microarray analysis). The gels were developed using PhosphorImager (Molecular Dynamics). S1 analysis was done with the following 32P-labeled oligonucleotides: Hprt S1: 5′-TCTTCAGTCTGATAAAATCTACAGTCATAGGAATGGATCTATCACTATTTCTATTCAGTGATTACATTAAAG-3′, Sepw1 S1: 5′-TTCAACCGGGAACACCTGGAAACATGGCTGCCTGTCTTCTTGAAGTCTTGAGGTGGAAAGGGAAAGCAAAGCAGGAGGGTTTTCCCACCC-3′.