Table 1 Verification of microarray analysis by Real Time – Polymerase Chain Reaction: In order to evaluate the SN-38-mediated activation of pro-apoptotic pathways, we confirmed the microarray results with real-time PCR using total RNA from 18 h post SN-38 exposure of the SW-620 cells and control. Primer express software from ABI has been used to design the primers for real-time PCR (amplicon sizes were about 70 bp). Gene symbols and Probe Set ID numbers are as found at the NCBI website http://www.ncbi.nlm.nih.gov and NetAffx™ Analysis Center http://www.affymetrix.com/analysis/index.affx. Data are averages from two separate experiments, each in duplicate. Data are reported as the fold change of gene expression level SN-38 treated cells versus no treatment control. FC = fold change.
From: SW-620 cells treated with topoisomerase I inhibitor SN-38: gene expression profiling
Gene Symbol | Affymetrix Probe Set ID | Primer for RT-PCR | RT-PCR avg. FC | Microarray avg. FC |
|---|---|---|---|---|
β-actin | NM_001101 | F: CGATCCACACGGAGTACTTG R: GGATGCAGAAGGAGATCACTG | NC | NC |
RGC32 | 218723_s_at | F: GAAGCCTTCATTGCTGATCTTG R: GTCCTCGGAACTTTCTGAAGCT | 6.2 | 6.5 |
ITGB7 | 205718_at | F: CGGCTCTCGGTGGAAATCTAT R: GGTCGTGATGGCACTTTTGTAG | 3.1 | 7.8 |
PDCD4 | 202731_at | F: GTGCTGGAGCGGTTTGTAGAA R: CCTTCGCTTACAAAACGCTTTC | 1.8 | 2.5 |
ABAT | 209459_s_at | F: CTGTTGGTTCAACGTGGTTTCC R: GCATTTCGGTATCATCTGCCTG | 3.4 | 6.7 |
DKK3 | 214247_s_at | F: ACCCCTGTCCAGATTATTGGC R: TTGTTTCCATCTCCTCCCCTC | 4.4 | 6 |
LYZ | 213975_s_at | F: CGCTACTGGTGTAATGATGGCA R: CAAGCTACAGCATCAGCGATGT | 4.6 | 11 |
CCL20 | 205476_at | F: GTCTGTGTGCGCAAATCCAA R: CCATTCCAGAAAAGCCACAGTT | 3.6 | 10.6 |
UBD | 205890_s_at | F: TTGCAATGGAAAGAGACTGGAA R: AGGAAGAGTAAGTTGCCCTTTCTG | 28.2 | 17.9 |
FGF3 | 214571_at | F: AATCAGGGTCCAGTGGGAACT R: CAAATGCCCTGCATTGCA | -12.6 | -5.1 |
FAF1 | 218080_x_at | F: CGGTGGAACCAGCCATTC R: TTGGCGAGGAGCCCTTCT | -4.8 | -5.1 |
HIST1H2BK | 208527_x_at | F:TACGTGTACAAGGTGCTGAAACAG R: CATGATCCCCATGGCTTTAGA | -8.6 | -6.1 |
Cyclin E1 | 213523_at | F: CACCAGCCACCTCCAGACA R: GTGGGAGTCCCTTAGGTCAACTAG | 3.1 | 2.2 |
Cyclin E2 | 205034_at | F:GAAGTAGCCGTTTACAAGCTAAGCA R: GCCTGGATTATCTGGGCTTCT | 3.2 | 4.1 |
TNFRSF6 | 216252_x_at | F: AATCATCAAGGAATGCACACTCA R: AAGCCACCCCAAGTTAGATCTG | 4.2 | 4.5 |