Table 5 of Brooks, Mol Vis 2011; 17:3034-3054.

Table 5. Quantitative expression profiles of housekeeping genes obtained by qRT–PCR and RNA-seq

Transcript Gene ID Description WT FPKM Nrl−/− FPKM RNA-seq FC WT Ct Nrl−/− Ct qPCR FC
NM_007393 Actb Actin, b 136.24 128 −1.07 19.61 19.84 −1.17
NM_020559 Alas1 Aminolevulinic acid synthase 1 8.06 8.46 1.05      
NM_009735 B2m β 2-microglobulin 11.88 20.11 1.71 25.67 25.09 1.5
NM_019468 G6pd2 Glucose-6-phosphate dehydrogenase 2 9.85 12.13 1.23      
NM_008084 Gapdh Glyceraldehyde-3-phosphate dehydrogenase 6.68 4.47 −1.49 17.64 18.09 −1.37
NM_010368 Gusb b-glucuronidase 3.63 4 1.1 28.72 28.67 1.03
NM_008194 Gyk Glycerol kinase 2.62 2.69 1.02      
NM_001110251 Hmbs
(isoform 2) Hydroxymethylbilane synthase 3.16 3.25 1.03      
NM_013551 Hmbs
(isoform 1) Hydroxymethylbilane synthase 1.89 2.1 1.11      
NM_013556 Hprt Hypoxanthine guanine phosphoribosyl transferase 47.5 65.34 1.37 22.61 22.58 1.02
NM_008302 Hsp90ab1 Heat shock protein 90 kDa α class B member 1 149.09 199.47 1.33 22.51 22.25 1.2
NM_001081113 Ipo8 Importin 8 10.48 11.31 1.08      
NM_023144 Nono Non-POU-domain-containing octamer-binding 28.64 38.59 1.35      
NM_008828 Pgk1 Phosphoglycerate kinase 1 17.88 16.91 −1.06 20.86 21.05 −1.15
NM_009089 Polr2a Polymerase (RNA) II (DNA directed) polypeptide A 50.56 36.5 −1.39      
NM_008907 Ppia Peptidylprolyl isomerase A (cyclophilin A) 2.38 2.68 1.13      
NM_009438 Rpl13a Ribosomal protein L13A 45.25 44.63 −1.01 20.22 20.62 −1.32
NM_007475 Rplp0 Ribosomal protein large P0 39.12 39.67 1.02      
NM_026020 Rplp2 Ribosomal protein large P2 18.51 17.15 −1.07      
NM_013765 Rps26 Ribosomal protein S26 22.94 21.71 −1.06 21.7 21.94 −1.19
NM_023281 Sdha Succinate dehydrogenase complex subunit A, flavoprotein 74.03 80.45 1.09      
NM_013684 Tbp TATA box binding protein 18.51 18.9 1.02 25 25.24 −1.18
NM_011638 Tfrc Transferrin receptor 34.3 37.53 1.09      
NM_011654 Tuba2 Tubulin, α 2 37.53 46.85 1.25      
NM_009451 Tubb4 Tubulin β 4 79.34 80.45 1.01 23.13 23.45 −1.25
NM_019639 Ubc Ubiquitin C 33.13 27.86 −1.19 28.29 29.21 −1.89
NM_011740 Ywhaz Tyrosine 3-monooxygenase-tryptophan 5-monooxygenase activation protein z polypeptide 38.05 51.98 1.37      

We evaluated housekeeping genes (HKGs) for their expression in RNA-seq data and by qRT–PCR analysis. Rows in bold indicate genes that are significantly differentially expressed and hence not good choices for HKGs. WT=wild type, Ct=crossing threshold, FPKM=fragments per kilobase of exon model per million mapped reads.

Brooks, Mol Vis 2011; 17:3034-3054. http://www.molvis.org/molvis/v17/a327

©2011 Molecular Vision http://www.molvis.org/molvis/

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