Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

Bernasconi, Michele; Berger, Christoph; Sigrist, Jürg A; Bonanomi, Athos; Sobek, Jens; Niggli, Felix K; Nadal, David

doi:10.1186/1743-422X-3-43

Virology Journal

Table 2 Expression profiles of 17 housekeeping genes in a panel of cell lines

From: Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

	B95.8			BJAB			Namalwa			Raji			Akata			Jijoye			P3HR1			All cell lines
High expression	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV
RPL37A	0.36	0.05	0.15	0.33	0.02	0.06	1.31	0.18	0.14	0.27	0.21	0.76	1.69	0.02	0.01	2.05	0.01	0.01	1.35	0.05	0.04	1.10	0.68	0.62
KIAA0220	0.06	0.01	0.12	2.33	0.60	0.26	1.56	0.07	0.05	2.98	0.79	0.27	1.64	0.03	0.02	2.02	0.01	0.01	1.37	0.02	0.01	1.63	0.87	0.54
CLU	1.62	0.02	0.01	0.21	0.04	0.21	0.06	0.03	0.41	n.d.		0.00	0.13	0.04	0.33	0.20	0.06	0.28	0.20	0.02	0.12	0.26	0.59	2.24
MTA2	0.00	0.01	12.49	0.02	0.02	1.13	n.d.		0.00	n.d.		0.00	n.d.		0.00	n.d.		0.00	n.d.		0.00
384D8-2.2	0.27	0.05	0.17	0.32	0.04	0.13	0.35	0.04	0.11	n.d.		0.00	0.36	0.06	0.16	0.70	0.21	0.30	0.64	0.04	0.07	0.29	0.43	1.47
Constant expression	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV
FTL	1.49	0.08	0.05	0.20	0.01	0.05	0.10	0.05	0.54	n.d.		0.00	0.33	0.12	0.36	0.51	0.25	0.49	0.75	0.10	0.13	0.45	0.59	1.31
*PSMD2*	0.89	0.04	0.04	2.38	0.67	0.28	1.08	0.05	0.04	0.24	0.01	0.06	1.67	0.02	0.01	1.46	0.20	0.14	1.04	0.15	0.14	1.22	0.63	0.52
*PSMB3*	1.49	0.02	0.01	2.35	0.62	0.27	1.61	0.12	0.08	0.62	0.22	0.36	1.70	0.00	0.00	2.03	0.00	0.00	1.35	0.04	0.03	1.57	0.51	0.33
*TCLF1*	0.53	0.02	0.03	0.72	0.01	0.02	1.43	0.13	0.09	0.20	0.06	0.30	0.51	0.21	0.42	1.26	0.32	0.25	1.18	0.11	0.09	0.90	0.40	0.52
H3F3A	1.71	0.03	0.02	2.44	0.76	0.31	1.64	0.13	0.08	7.38	4.68	0.63	1.69	0.00	0.00	2.08	0.01	0.01	1.35	0.04	0.03	2.44	2.03	0.83
*PTDSS1*	1.40	0.00	0.00	2.45	0.76	0.31	1.51	0.07	0.04	4.87	1.42	0.29	0.95	0.02	0.02	1.92	0.09	0.05	1.35	0.03	0.02	1.98	1.25	0.53
KARS	1.19	0.03	0.03	2.45	0.77	0.31	1.62	0.12	0.07	6.40	3.35	0.52	1.66	0.02	0.01	2.08	0.01	0.00	1.35	0.05	0.03	2.22	1.75	0.79
*AAMP*	0.57	0.01	0.02	0.62	0.01	0.01	0.59	0.04	0.07	0.13	0.04	0.31	0.55	0.07	0.12	1.00	0.18	0.18	1.29	0.02	0.01	0.71	0.35	0.50
Common	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV	Mean	SD	CV
*βactin.sense(ACTB*)	1.73	0.04	0.02	1.68	0.28	0.17	1.21	0.07	0.06	2.28	0.23	0.10	0.78	0.13	0.16	1.72	0.24	0.14	1.34	0.01	0.00	1.49	0.46	0.31
*βactin.70 mer(ACTB*)	1.69	0.02	0.01	1.00	0.24	0.24	1.42	0.04	0.02	1.16	0.05	0.05	1.65	0.01	0.01	1.44	0.01	0.01	1.33	0.05	0.04	1.37	0.23	0.17
*c-yes.70 mer*	1.32	0.02	0.02	2.05	0.42	0.20	1.51	0.12	0.08	0.92	0.12	0.13	1.70	0.02	0.01	2.05	0.00	0.00	1.35	0.06	0.04	1.67	0.61	0.37
c-yes.2	0.45	0.05	0.10	0.11	0.03	0.32	n.d.		0.00	n.d.		0.00	0.05	0.01	0.28	0.13	0.01	0.11	0.08	0.01	0.11
MHCL.70 mer	1.73	0.05	0.03	0.48	0.13	0.27	1.57	0.07	0.05	0.80	0.01	0.01	1.69	0.02	0.01	0.04	0.04	1.18	1.27	0.02	0.02	1.10	0.62	0.55
*HMBS.2*	1.03	0.02	0.13	2.42	0.72	0.30	1.59	0.10	0.06	2.57	0.39	0.15	1.47	0.03	0.02	1.97	0.05	0.03	1.35	0.05	0.04	1.52	0.33	0.22

CV: coefficient of variation; n.d.: not detected.; SD: Standard deviation; bold letters indicate gene-sets that were considered to be constantly detectable across cell lines, and were selected to be used as normalization-set in further experiments. Probe sets that showed a CV < 0.6 were selected for the normalization housekeeping gene set.

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ISSN: 1743-422X

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