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.