Table 5 |
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Characteristics of gene specific real-time PCR assays. |
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Experimentally derived genes |
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|
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Gene symbol |
Accession |
Amplicon size (bp) |
PCR efficiency |
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|
|
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|
DNAJC17 |
DnaJ (Hsp40) homolog, subfamily C, member 17 |
NM_001046276 |
Left primer |
TCTGAAGATTTCCTGGTTGGA |
90 |
1.92 |
|
Right Primer |
CTCTCGGACACCACTGAGC |
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|
Probe |
#57: GGCCCCAG |
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|
|
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|
HDAC1 |
histone deacetylase 1 |
NM_001037444 |
Left primer |
GGATGAGAAAGAGAAAGATCCAGA |
76 |
1.53 |
|
Right Primer |
TTCTTGCTTCTCTTCCTTGGTT |
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|
Probe |
#35:AGAAGAGGA |
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|
|
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|
RANBP10 |
RAN binding protein 10 |
NM_001098125 |
Left primer |
CTCAACAGCGCCATTTTAGA |
94 |
1.81 |
|
Right Primer |
CCATGAGCCGTAGACATTCA |
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|
Probe |
#37:TGCCCTGG |
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|
|
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|
CNOT7 |
CCR4-NOT transcription complex, subunit 7 |
NM_001034312 |
Left primer |
GATAGGACCGCAGCATCAG |
111 |
1.82 |
|
Right Primer |
CCACAATATTTGGCATCATCA |
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|
Probe |
#100:GCTCACAG |
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|
|
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|
ACTR1A |
ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) |
XM_879421 |
Left primer |
TATCTGCACCGCAGGAGAG |
96 |
1.54 |
|
Right Primer |
CCTTCTTAGAGACCCACATCTTCT |
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|
Probe |
#130:CTGGACAC |
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|
|
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|
BBS2 |
Bardet-Biedl syndrome 2 |
NM_001038160 |
Left primer |
GAGCAGGTCATCTGCGTGT |
132 |
1.90 |
|
Right Primer |
TCCCCTCCTAAGAAGAAGCTGT |
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|
Probe |
#150:TGCTGTTC |
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|
|
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|
SUZ12 |
suppressor of zeste 12 homolog (Drosophila) |
XM_582605 |
Left primer |
GAACACCTATCACACACATTCTTGT |
130 |
1.99 |
|
Right Primer |
TAGAGGCGGTTGTGTCCACT |
|||||
|
Probe |
#150:GAACAGCA |
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|
|
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|
ZNF131 |
zinc finger protein 131 |
NM_001101218 |
Left primer |
AGAAAGAAGCTTTATGAATGTCAGG |
94 |
1.90 |
|
Right Primer |
GTTTATCTCCAGTGTGTATCACCAG |
|||||
|
Probe |
#33:AGCTGGGA |
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|
|
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|
SLC30A6 |
solute carrier family 30 (zinc transporter), member |
NM_001075766 |
Left primer |
CAGTTGGACAAACTTATCAGAGAGG |
66 |
1.90 |
|
Right Primer |
ATGCTCATTTCGGACTTCCA |
|||||
|
Probe |
#58:GGATGGAG |
|||||
|
|
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|
C2ORF29 |
LOC506268 similar to Uncharacterized protein C2orf29 |
XM_582695 |
Left primer |
CCTTCAAGAGCCCCCTGT |
64 |
1.96 |
|
Right Primer |
GGGTCCTTTTCCAACTCTCC |
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|
Probe |
#73:TCCTCAGC |
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|
|
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|
Literature derived genes |
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|
|
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|
Gene symbol |
Accession |
|||||
|
|
||||||
|
RPS9 |
ribosomal protein S9 |
NM_001101152 |
Left primer |
TGAGGATTTCTTGGAGAGACG |
126 |
1.97 |
|
Right Primer |
ATGTTCACCACCTGCTTGC |
|||||
|
Probe |
#138:ATCCACCA |
|||||
|
|
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|
UXT |
ubiquitously-expressed transcript |
NM_001037471 |
Left primer |
AACTTCTTCGTTGACACAGTGG |
130 |
2.01 |
|
Right Primer |
CTGTGAGGAGACTGCTCTTACG |
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|
Probe |
#29:GGCAGAAG |
|||||
|
|
||||||
|
GAPDH |
glyceraldehyde-3-phosphate dehydrogenase |
NM_001034034 |
Left primer |
GAAGCTCGTCATCAATGGAAA |
67 |
1.94 |
|
Right Primer |
CCACTTGATGTTGGCAGGAT |
|||||
|
Probe |
#9:CATCACCA |
|||||
|
|
||||||
|
PPIA |
peptidylprolyl isomerase A (cyclophilin A) |
NM_178320 |
Left primer |
GTCAACCCCACCGTGTTCT |
99 |
1.94 |
|
Right Primer |
TTCTGCTGTCTTTGGAACTTTG |
|||||
|
Probe |
#152:GACGGCGA |
|||||
|
|
||||||
|
RPS15A |
ribosomal protein S15a |
NM_001037443 |
Left primer |
TCAGCCCTAGATTTGATGTGC |
104 |
1.85 |
|
Right Primer |
GCCAGCTGAGGTTGTCAGTA |
|||||
|
Probe |
#32:CTGCTCCC |
|||||
|
|
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|
Gene of interest |
||||||
|
|
||||||
|
Gene symbol |
Accession |
|||||
|
|
||||||
|
OXTR |
Oxytocin receptor |
NM_174134 |
Left primer |
CGTGCAGATGTGGAGTGTCT |
96 |
1.99 |
|
Right Primer |
TTGCAGCAGCTGTTGAGG |
|||||
|
Probe |
#162:TCCTGGC |
|||||
|
|
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|
Roche Universal probe library assays were designed for 15 candidate endogenous control genes including 10 experimentally derived genes, five commonly used genes and one target gene - OXTR. |
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|
Walker et al. BMC Molecular Biology 2009 10:100 doi:10.1186/1471-2199-10-100 |
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