Validation of oligoarrays for quantitative exploration of the transcriptome

Nygaard, Vigdis; Liu, Fang; Holden, Marit; Kuo, Winston P; Trimarchi, Jeff; Ohno-Machado, Lucila; Cepko, Connie L; Frigessi, Arnoldo; Glad, Ingrid K; van de Wiel, Mark A; Hovig, Eivind; Lyng, Heidi

doi:10.1186/1471-2164-9-258

BMC Genomics

Table 2 Transcript concentration of selected genes in adult mouse retina¹

From: Validation of oligoarrays for quantitative exploration of the transcriptome

UniGene ID	Gene Symbol	Gene name	Oligoarray	MPSS	SAGE	qRT-PCR
Genes with high expression
Mm.371592	Ubb	Ubiquitin B	9705	401	435	NA
Mm.368524			8916	3180	722	NA
Mm.47709	Pdc	Phosducin	6027	516	425	10.36
Mm.151562	Rbp3	Retinol binding protein 3	5733	1292	657	4.77
Mm.16224	Guca1a	Guanylate cyclase activator 1a (retina)	5366	611	546	0.66
Mm.284811	Unc119	Unc-119 homolog (C.elegans)	4812	335	1046	2.40
Mm.59151	Guca1b	Guanylate cyclase activator 1B	4478	3116	287	1.44
Mm.235863			4046	1312	361	NA
Mm.285993	Calm1	Calmodulin 1	3304	543	222	3.09
Mm.28643	Vamp2	Vesicle-associated membrane protein2	3250	683	296	2.63
Mm.16831	Ckb	Creatine kinase, brain	2896	1164	620	NA
Mm.223674	Syp	Synaptophysin	2592	595	130	0.16
Mm.1372	Pde6b	Diesterase 6B, cGMP, rod reseptor, beta polypeptide	2400	956	982	1.73
Mm.156506	Pcdh21	Protocadherin 21	2137	570	232	1.80
Mm.297482	Tpt1	Tumor protein, translationally controlled 1	1742	359	750	1.44
Mm.3667	Vtn	Vitronectin	1630	634	398	1.74
Mm.352239	Gpsn2	Glycoprotein, synaptic 2	1579	484	287	0.02
Mm.55143	Dkk3	Dickkopf homolog 3 (Xenopus laevis)	1576	266	185	0.10
Mm.726	Bsg	Basigin	1490	870	268	0.87
Mm.683			1472	236	407	NA
Mm.28147	Reep6	Receptor accessory protein 6	1394	1229	445	3.42
Mm.273538		cDNA, clone Y1G0119M19	1389	375	259	NA
Mm.16228	Slc25a4	Solute carrier family 25, member 4	1382	520	416	0.67
Mm.235204	Atp1b2	ATPase, Na+/K+ transporting, beta 2 polypeptide	1210	466	213	1.79
Mm.94160	Bex2	Brain expressed X-linked 2	1171	339	139	0.09
Mm.331	Ubc	Ubiquitin C	1165	423	130	NA
Mm.26633	Plekhb1	Pleckstrin homology domain containing, family B member 1	931	474	620	0.32
Mm.305152	Apoe	Apolipoprotein E	920	1046	213	0.25
Mm.200608	Clu	Clusterin	885	456	222	0.07
Mm.278865	Stxbp1	Syntaxin binding protein 1	873	512	389	0.60
Mm.236513	Pcbp2	Poly(rC) binding protein 2	777	401	325	1.78
Mm.41926			698	271	130	NA
Mm.373613			661	340	268	NA
Mm.379381			650	261	278	NA
Mm.197518	Laptm4b	Lysosomal-associated protein transmembrane 4B	634	451	352	0.30
Genes with low expression
Mm.24678	Pard6g	Par-6 partitioning defective 6 homolog gamma (C. elegans)	13	2	9	0.01
Mm.273155	2610110G12Rik	RIKEN cDNA 2610110G12 gene	14	2	9	0.00
Mm.1249	Lamc1	Laminin, gamma 1	14	1	9	NA
Mm.261831			19	1	9	NA
Mm.257952	Tmem159	Transmembrane protein 159	20	2	9	0.01

¹The 40 transcripts in common for oligoarrays, MPSS and SAGE among two subsets of 100 genes each, one with the highest and another with the lowest transcript concentrations. The values are listed as number of transcripts per cell for oligoarrays, MPSS and SAGE, and as relative to the endogenous control β-actin (Actb) for qRT-PCR. NA means not analysed.

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ISSN: 1471-2164

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