Table 1 Oligonucleotide sequences for real-time PCR based DNA copy number determination (GCN) and gene expression analysis (GXP): Primer sequences for known genes are submitted to RTPrimerDB [37, 38]. Proper DNase treatment (see Methods) allows the use of intra-exonic primer pairs for both DNA and RNA profiling (F: forward primer; R: reverse primer).
APPLICATION | GENE/CLONE | PRIMER SEQUENCES (5' > 3') | |
|---|---|---|---|
GCN | MYCN | RTPrimerDB ID 11 | |
GXP | MYCN | RTPrimerDB ID 180 | |
GCN | DDX1 | RTPrimerDB ID 12 | |
GXP | DDX1 | RTPrimerDB ID 93 | |
GCN | NAG | RTPrimerDB ID 13 | |
GXP | NAG | RTPrimerDB ID 114 | |
GCN + GXP | g10e3 | F | CTTTTCCTAAGAGCAAGGAAACAGA |
R | CTGTTATTTAAAGAAACCAGCATTCACT | ||
GCN + GXP | g9d9 | F | CTTTGGCCAGTTCCACAGTTC |
R | CACACCCAGCCTTAAGTTTTTGA | ||
GCN + GXP | NSE1 | RTPrimerDB ID 715 | |
GCN + GXP | g10d12 | F | ACCTTCCATCCACACCTATGCT |
R | TTTCATTCAGTTCAGTCTTCATCGA | ||
GCN + GXP | DNMT3A | RTPrimerDB ID 713 | |
GCN + GXP | TEM8 | RTPrimerDB ID 712 | |
GCN + GXP | BMP10 | RTPrimerDB ID 717 | |
GCN + GXP | PLEK | RTPrimerDB ID 716 | |
GCN + GXP | PPP3R1 | RTPrimerDB ID 718 | |
GCN + GXP | g4d5 | F | AGATGCCCATTTCATCTCTCTTG |
R | TGCTACAGGTCTTGCATTATCAAAC | ||
GCN + GXP | ETAA16 F | RTPrimerDB ID 714 | |
GCN + GXP | MEIS1 | RTPrimerDB ID 690 | |
GCN + GXP | g2h10 | F | TTCCTGATGCCCACAAAGTTTA |
R | ACACAAACTCTGAAAGCCAACTAATTT | ||