Table 2. Number of different repetitive elements represented by complementary probes in mouse gene expression microarray platforms.

	Mouse Genome	Illumina			Affymetrix
	mm9 assembly	WG-6 v1.0	WG-6 v1.1	WG-6 v2.0	U74Av2	430 2.0
LINE	122 elements	70 elements	71 elements	66 elements	62 elements	97 elements
	1.3 million loci	351 probes	358 probes	321 probes	631 probes	4635 probes
SINE	41 elements	30 elements	30 elements	32 elements	32 elements	37 elements
	2.1 million loci	473 probes	486 probes	558 probes	1465 probes	11650 probes
LTR	471 elements	153 elements	155 elements	153 elements	107 elements	291 elements
	1.2 million loci	393 probes	396 probes	372 probes	1362 probes	7293 probes
DNA	156 elements	42 elements	43 elements	40 elements	36 elements	88 elements
	0.2 million loci	69 probes	71 probes	58 probes	229 probes	1329 probes
Satellite	8 elements	2 elements	2 elements	2 elements	2 elements	2 elements
	0.01 million loci	55 probes	54 probes	61 probes	266 probes	463 probes
Simple	315 elements	8 elements	3 elements	9 elements	26 elements	47 elements
	1.5 million loci	9 probes	9 probes	12 probes	67 probes	168 probes
Other	108 elements	13 elements	14 elements	13 elements	15 elements	32 elements
	0.6 million loci	47 probes	51 probes	56 probes	219 probes	586 probes
Total	1,221 elements	318 elements	323 elements	315 elements	280 elements	594 elements
	6.9 million loci	1397 probes	1425 probes	1438 probes	4239 probes	26124 probes

Mouse genome data is derived from Repeatmasker annotation of the mm9 assembly of the sequenced genome downloaded from the UCSC genome browser [62]. The number of elements within each repetitive element class that are represented in the mouse genome and in the different microarray platforms is indicated. The number of genomic loci or microarray probes corresponding to each repetitive element class is also shown.