Table 1 Reference genes found on a typical Affymetrix 3’IVT microarray. Amplification and hybridization control RNAs are added in various proportions and quantities as indicated in the last column. The amplification control transcripts are added using various dilutions which results in an estimated copy numbers ranging from one copy per 6,667 to 100,000 transcripts in the studied RNA sample. The hybridization control consists of biotinylated and fragmented cRNAs added in various amounts that result in a final concentrations ranging from 1.5 to 100 pM
From: Microarray experiments and factors which affect their reliability
Group | Type | Name | Description |
|---|---|---|---|
1 | Housekeeping genes | AFFX-HSAC07/X00351 | ACTB - β-actin gene responsible for the structure of the cell |
AFFX-HUMGAPDH/M33197 | GAPDH – enzyme which takes part in glycolysis | ||
AFFX-HUMISGF3A/M97935 | STAT1 – transcription factor | ||
2 | Ribosomal RNA | AFFX-HUMRGE/M10098 | Gene coding for 18S rRNA subunit |
AFFX-M27830 | Gene coding for 28S rRNA subunit | ||
AFFX-r2-Hs18SrRNA | Gene coding for 18S rRNA subunit - version 2 | ||
AFFX-r2-Hs28SrRNA | Gene coding for 28S rRNA subunit - version 2 | ||
3 | Amplification control (Poly-A spike) | AFFX-DapX / AFFX-r2-Bs-dap | Dap gene of B.Subtilis bacteria - proportions 1:6,667 |
AFFX-ThrX / AFFX-r2-Bs-thr | Thr gene of B.Subtilis bacteria - proportions 1:25,000 | ||
AFFX-PheX / AFFX-r2-Bs-phe | Phe gene of B.Subtilis bacteria - proportions 1:50:000 | ||
AFFX-LysX / AFFX-r2-Bs-lys | Lys gene of B.Subtilis bacteria - proportions 1:100,000 | ||
4 | Hybridization control (Bacterial spike) | AFFX-BioB / AFFX-r2-Ec-bioB | BioB gene of E.Coli bacteria – quantity 1.5 pM |
AFFX-BioC / AFFX-r2-Ec-bioC | BioC gene of E.Coli bacteria – quantity 5 pM | ||
AFFX-BioDn / AFFX-r2-Ec-bioD | BioD gene of E.Coli bacteria – quantity 25 pM | ||
AFFX-CreX / AFFX-r2-P1-cre | Cre gene of P1 bacteriophage – quantity 100 pM |