| Literature DB >> 21303565 |
Christine J Piek1, Bas Brinkhof, Jan Rothuizen, Aldo Dekker, Louis C Penning.
Abstract
BACKGROUND: The dog is frequently used as a model for hematologic human diseases. In this study the suitability of nine potential reference genes for quantitative RT-PCR studies in canine whole blood was investigated.Entities:
Year: 2011 PMID: 21303565 PMCID: PMC3045956 DOI: 10.1186/1756-0500-4-36
Source DB: PubMed Journal: BMC Res Notes ISSN: 1756-0500
Abbreviations, GenBank Accession numbers, names, and chromosomal location of canine candidate reference genes evaluated.
| Gene | Name | Chromosomal location in | |
|---|---|---|---|
| RPS19 | Ribosomal protein S19 | Chromosome 1 | |
| RPL8 | Ribosomal protein L8 | Chromosome 13 | |
| RPS5 | Ribosomal protein S5 | Chromosome 1 | |
| GUSB | Beta-Glucuronidase | Chromosome 6 | |
| B2M | Beta-2-microglobulin | Chromosome 30 | |
| HNRNPH | Heterogeneous nuclear ribonucleoprotein H | Chromosome 11 | |
| HPRT | Hypoxanthine phosphoribosyltransferase 1 | Chromosome X | |
| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | Chromosome X | |
| SRPR | Signal recognition particle receptor | Chromosome 5 |
Primer sequences, exon locations, amplicon size, and optimal melting temperature of canine candidate reference genes.
| Gene | Forward 5' →3'* | Exon(s) | Reverse 5' → 3' | Exon(s) | Product length (bp) | |
|---|---|---|---|---|---|---|
| RPS19 | CCTTCCTCAAAAA/GTCTGGG | 2/3 | GTTCTCATCGTAGGGAGCAAG | 3 | 95 | 61.0 |
| RPL8 | CCATGAAT/CCTGTGGAGC | 4/5 | GTAGAGGGTTTGCCGATG | 5 | 64 | 55.0 |
| RPS5 | TCACTGGTGAG/AACCCCCT | 2/3 | CCTGATTCACACGGCGTAG | 3 | 141 | 62.5 |
| GUSB | AGACGCTTCCAA/GTACCCC | 3/4 | AGGTGTGGTGTAGAGGAGCAC | 4 | 103 | 62.0 |
| B2M | TCCTCATCCTCCTCGCT | 1 | TTCTCTGCTGGGTGTCG | 2 | 85† | 61.2 |
| HNRNPH | CTCACTATGATCCACCACG | 5 | TAGCCTCCATAAC/CTCCAC | 5/6 | 151 | 61.2 |
| HPRT | AG/CTTGCTGGTGAAAAGGAC | 5/6 | TTATAGTCAAGGGCATATCC | 7 | 114‡ | 56.0 |
| GAPDH | TGTCCCCACCCCCAATGTATC | 2 | CTCCGATGCCTGCTTCACTACCTT | 2 | 100 | 58.0 |
| SRPR | GCTTCAGGATCTGGACTGC | 5/6 | GTTCCCTTGGTAGCACTGG | 6 | 81 | 61.2 |
* If a primer is located on two exons, the junctions are shown with a dividing forward slash (/).
† Genomic product size would be approximately 3.6 kb.
‡ Genomic product size would be approximately 300 bp.
Figure 1Real-time PCR cycle threshold numbers (Cq values) for nine potential reference genes in 4 disease categories (n = 263) . Real-time PCR cycle threshold numbers (Cq values) are plotted for nine potential reference genes. Group A included 6 healthy dogs, group B 85 dogs within 24 hours after a surgical procedure, group C 107 dogs with miscellaneous internal diseases, and group D 65 dogs with hematologic diseases. Statistically significant differences between mean Cq of the disease categories are depicted. The boxes represent the two middle quartiles with medians. Whiskers delineate the range.
Relation of Cq and white blood cell count.
| Gene | Cq change for 10 fold increase in WBC count | p | WBC within reference range | Difference | p | |||
|---|---|---|---|---|---|---|---|---|
| Mean Cq | SD | Mean Cq | SD | |||||
| RPS19 | 0.92 | 0 | 17.35 | 0.82 | 17.90 | 1.31 | 0.56 | 0.002 |
| RPL8 | 0.52 | 0.006 | 19.20 | 0.67 | 19.52 | 1.14 | 0.32 | 0.026 |
| RPS5 | 1.06 | 0 | 18.30 | 0.86 | 19.01 | 1.61 | 0.71 | 0.0009 |
| 21.09 | 0.97 | 21.08 | 1.47 | |||||
| B2M | 1.28 | 0 | 15.85 | 0.86 | 16.58 | 1.74 | 0.73 | 0.0006 |
| 22.40 | 0.86 | 22.20 | 1.02 | |||||
| HPRT | - 0.87 | 0 | 21.14 | 0.93 | 20.71 | 1.03 | -0.43 | 0.01 |
| - 0.51 | 0.023 | 14.87 | 0.97 | 14.80 | 0.96 | |||
| 18.30 | 1.09 | 19.01 | 1.51 | |||||
• WBC = White Blood Cell Count
Change in Cq is given for a ten fold increase in WBC count, mean Cq and SD for dogs with WBC count in the reference range and for dogs with a leukocytosis with a WBC > 30*109/l.
Figure 2Pairwise variations between 2 sequential normalization factors including an increasing number of potential reference genes . To determine the optimal number of reference genes, first the geometric mean of the expression of the previously ranked genes was calculated and then pair wise variations between sequential normalisation factors were calculated. Using the cut-off recommended by GeNorm of 0.15 the optimal number of reference genes for the data set in this study would be at least 5.
Ranking of potential reference genes according to their expression stability by GeNorm and Normfinder.
| GeNorm | Stability measure* | Normfinder | Stability Value* | Normfinder | Stability Value* |
|---|---|---|---|---|---|
| M | Disease category** | WBC quartiles*** | |||
| RPL8 and RPS19 | 0.55 | RPL8 | 0.16 | RPL8 | 0.09 |
| HNRNPH | 0.17 | HNRNPH | 0.14 | ||
| RPS5 | 0.64 | SRPR | 0.19 | GUSB | 0.14 |
| GUSB | 0.78 | GUSB | 0.26 | SRPR | 0.16 |
| B2M | 0.87 | HPRT | 0.26 | GAPDH | 0.17 |
| HNRNPH | 0.93 | RSP19 | 0.26 | RSP19 | 0.17 |
| HPRT | 0.99 | B2M | 0.28 | RPS5 | 0.21 |
| GAPDH | 1.01 | RPS5 | 0.32 | HPRT | 0.21 |
| SRPR | 1.03 | GAPDH | 0.35 | B2M | 0.21 |
*Genes are ranked according to decreasing expression stability.