Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

Paolacci, Anna R; Tanzarella, Oronzo A; Porceddu, Enrico; Ciaffi, Mario

doi:10.1186/1471-2199-10-11

BMC Molecular Biology

Table 2 List of 32 UniGene clusters and corresponding TCs selected for qRT-PCR analysis of their expression.

From: Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

Unigene Cluster	Gene annotation	CV TPM	NS UniGene	Rank UniGene	TIGR contig	TIGR freq.	Rank TIGR
1) Ta54963	GABARAP (GABA-receptor-associated protein)	9.85	356	1	TC304353, TC304722, TC295997	66/197	29
2) Ta54171	Superoxide dismutase [Cu-Zn]	11.95	1316	2	TC317053, TC294760, TC297148	110/197	8
3) Ta50503	Ubiquitin	12.79	1088	3	TC278495, TC296829, TC280981	72/197	22
4) Ta2776	Similar to RNase L inhibitor-like protein	13.17	158	4	TC278756, TC314244	38/197	91
5) Ta54733	Protein of unknown function (DUF 866)	15.47	167	5	TC335842, TC286574	40/197	86
6) Ta54948	Rab GTPase homolog (Rab7 subfamily)	16.22	366	6	TC278352, TC303984	33/197	110
7) Ta30797	Similar to phosphogluconate dehydrogenase	17.27	138	9	TC279294, TC284282	25/197	143
8) Ta35284	Protein transport protein Sec23A	17.95	101	10	TC278525	31/197	116
9) Ta54447	Acetyl-CoA acyltransferase	18.47	365	13	TC279279, TC283613	65/197	32
10) Ta54448	Protein of unknown function (DUF52 family)	19.24	99	15	TC279558	36/197	96
11) Ta 22845	ATP-depend. 26S proteasome regulatory sub.	20.48	186	24	TC353778	64/197	33
12) Ta659	Translation elongation factor 1 alpha-subunit	29.67	3026	94	TC288390	139/197	1
13) Ta30768	GAPDH (Glyceraldehyde-3-phosph. dehydrog.)	22.68	1807	32	TC304401, TC348958, TC310664, TC326825	137/197	2
14) Ta53919	S-adenosylmethionine decarboxylase	24.73	2533	47	TC320440, TC279487	135/197	3
15) Ta35497	Peptidyl-prolyl cis-trans isomerase (Cyclophilin)	30.81	2131	107	TC348130, TC348051, TC352472	135/197	4
16) Ta53937	Cytosolic malate dehydrogenase	24.58	1368	45	TC300803, TC279938	127/197	5
17) Ta53891	Zn-finger, A20-like domain containing protein	25.19	1291	50	TC293469	126/197	6
18) Ta45379	ADP-ribosylation factor	24.90	1180	48	TC337136	118/197	7
19) Ta1698	NADP-isocitrate dehydrogenase	24.39	761	42	TC283369, TC282416	95/197	10
20) Ta27771	60S ribosomal protein L18a-1	31.94	580	120	TC363506, TC298941	94/197	11
21) Ta53964	Translation elongation factor EF-1alpha (GTPase)	26.88	1074	68	TC279148	89/197	12
22) Ta54227	Cell div. control prot. (AAA-superfam. ATPases)	24.65	670	46	TC308517, TC281050	87/197	13
23) Ta54280	Translation initiation factor SuI1 family protein	23.53	609	36	TC297312, TC338691	82/197	15
24) Ta54512	Cytochrome b5 family protein	21.70	695	29	TC284040, TC283036, TC284818	77/197	17
25) Ta4045	Ubiquinol-cytochrome C reduct. iron-sulfur sub.	23.76	384	37	TC350975, TC327386	77/197	18
26) Ta53889	Hypothetical protein	29.95	603	97	TC317382, TC333515	74/197	19
27) Ta53967	Vacuolar ATP synthase 16 kDa proteolipid sub.	25.00	719	49	TC292895, TC344391	71/197	23
28) Ta44405	Beta-tubulin 4 (Tubb4)	22.94	114	33	TC278209	20/197	167
29) Ta54238	Ubiquitin-conjugating enzyme E2	28.67	165	86	TC295800, TC289972, TC289612	57/197	47
30) Ta38797	Similar to histone H3 (Arabidopsis)	33.94	1066	137	TC290356, TC280404, TC313660	68/197	27
31) Ta55512	Cathepsin B-like cysteine protease	24.55	171	43	TC311052, TC278654	52/197	53
32) Ta2291	ADP-ribosylation factor	38.31	377	162	TC278558, TC278370	66/197	31

Italics = novel reference genes; normal = traditional reference genes.
CV/TPM = Coefficient of Variation calculated on the expression values (TPMs) in six tissues (flower, inflorescence, leaf, root, seed and stem), UniGene Profile Viewer.
NS UniGene = Number of EST sequences included in each UniGene cluster.
Rank UniGene = Ranking of the UniGene clusters on the basis of the CV of their expression values (TPMs) in six wheat tissues.
TIGR frequency = Number of hosting libraries/total number of cDNA libraries, calculated for each TC or group of TCs linked to the selected UniGene clusters.
Rank TIGR = Ranking of the TCs or group of TCs linked to the selected UniGene clusters on the basis of their frequency.

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ISSN: 1471-2199

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