Table 2

Bioinformatic analysis of Content and distribution of Alu subfamilies among the PCR-1 and PCR-2 products Table legend text.

Alu subfamily

Bioinformatic analysis with the databasea

Analysis of bisulfite clone sequencings


Average CpG no.b

Copy no. of Alu

Copy no. of Alu matched to the primers for PCR-1

Clone no. of Alu obtained in the PCR-1 products

Total clone no. of Alu with methylated-CpG number ≥ 4 in the PCR-1 products

Clone no. of Alu obtained in the PCR-2 productsc


AluJ

16.3

29508 (6.2%)

28889 (6.1%)

52 (12.2%)

14 (6.3%)

3 (5.6%)

AluS

22.4

350888 (73.7%)

350419 (73.6%)

296 (69.3%)

156 (70.3%)

30 (55.6%)

AluY

24.5

95756 (20.1%)

91680 (19.3%)

79 (18.5%)

52 (23.4%)

21 (38.9%)


(Total)

22.4

476152 (100%)

470988 (100%)

427 (100%)

222 (100%)

54 (100%)


a476152 copies of Alu elements extracted bioinformatically from the NCBI database of human genome (C) as described (Ref. [13]);

b within the full sequence of Alu elements as illustrated in Figure 1A;

camplified from two representative samples with the primer set-2 after bisulfite modification

Xiang et al. BMC Cancer 2010 10:44   doi:10.1186/1471-2407-10-44

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