A custom microchip for the detection of all novel identified ncRNA candidates was generated by the company febit biomed gmbh (Heidelberg, Germany). In addition, probes for the detection of selected cellular ncRNA genes, including rRNA (5S, 5.8S), snRNAs, miscellaneous RNAs (7SL RNA, 7SK RNA, RNase MRP RNA, RNase P RNA, vault RNAs and Y RNAs), known human and EBV miRNAs (from miRBase; release 11.0; (Griffiths-Jones et al., 2006) as well as human snoRNAs (115 box C/D snoRNAs, 82 H/ACA snoRNAs, 25 scaRNAs; from snoRNA-LBME-database, version 3; (Lestrade & Weber, 2006) were included. DNA oligonucleotide probesets were designed using febit´s Geniom Client software.
Description
In total, approximately 4.300 probes of 30 nt in size or shorter, dependent on the cDNA sequence length, recognizing sense and antisense transcripts, as well as intra-array replicates were synthesized in situ on the microchip and analyzed with febit Geniom One technology (Supplementary Table 3) (Baum et al., 2003; Vorwerk et al., 2008). Sequence candidates longer than 30 nt were covered with multiple, overlapping probes.
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