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Table 1 Probe sets used in this study.

From: Rapid high-throughput analysis of DNaseI hypersensitive sites using a modified Multiplex Ligation-dependent Probe Amplification approach

Name

Probe1

Probe2

Genomic location

Product size

Gap size

N1

1AAGACAGAGTCAGCACCAAGCAACCTG

GAGCGGCTGCTTCTTTCTCTCTTGC2

chr2:234,440,746-234,440,797

94

-

N2

1GAGCAGCACTTAGTACACAGAGGCCTCTG

CCAGGATTGCAGAAGGCTTGCAGAGG2

chrX:153,258,524-153,258,587

106

9

N3

1GACCTTACTTTGATGAAGGCAGTTCTGC

CATGGGTGCCACGGTTTGAATGTATC2

chr21:33,073,083-33,073,161

121

25

N4

1CCCAGTGACCTACAGTAGAACTTTTCTGTGTCC

GCTGTTCTCCGTGCCTATCACCTGTTAAAGG2

chr2:234,444,778-234,444,867

132

26

N5

1CAAATAGTCGAGTGGTACCTGTTCAGCC

GACAGAACTAGGAAACAAATACCTCCTCATTCTATATGGC2

chr5:131,655,909-131,656,020

154

44

N6

1GACAGAAAATGCAGTCCAGTTGGTACAAGC

CTCTCTCAGGGCTGCTTCATGAACTTAC2

chr21:33,778,023-33,778,144

164

64

N7

1GCTGTTCAGCATTGGTGTAAGTTCTGATTCC

CTCCAGACACCTGAGCCAAGAGAAAGATT2

chr21:33,068,576-33,068,705

172

70

N8

1CTAAGGTGGCCATGCTTCTCTGGATTTGC

CAGCTCATCCCGCGTCGATTCCTGGAAGTGTTATC2

chr5:131,660,201-131,660,338

180

74

N9

1GGAAAGAGCAGGAGAAAGGGAATCTTGG

GTCTCTTCAGCTTGTGGGAACAAACGAG2

chr7:27,143,394-27,143,543

192

94

S1

1GTTTTGTACTGTGGGAGTCTGAGAGCGAG

GAGGTCCGAAAGCCGAATCACAGTC2

chr19:59,386,440-59,386,493

96

-

S2

1AGCTAAAGACGTTAGGAAACAGAGCAGGGTG

GTTGAACGGGAGTGCAGCACGGTTGT2

chr19:59,396,645-59,396,701

99

-

S3

1CGACTGCGAATTACTGTTTATGAGGTGACTC

GCTGGTTCTATCGGTGGACAGTGGGACATTC2

chr19:59,386,011-59,386,072

104

-

S4

1GGTACGGAAGGCAGAATCGTACCTG

CCTTACCAGGAAAACGGACAATCTTCC2

chr21:33,785,757-33,785,822

106

14

S5

1GCCACAAACTCAAATAGGAGACTCCGC

CGGTTTTCTATTGGCTAGAGCGGAGAAGC2

chr2:234,427,935-234,428,007

115

17

S6

1ATGGGGTACGACTTCGAATCACGTGC

CCTGATGACCTCTAGAGGTAAACTCGTGCAC2

chr7:27,149,886-27,149,967

124

25

S7

1AACCTAGTCCTCCCAGGTTAGCACG

CAGCCAGCCAACGCCTCTTCTGATTG2

chr19:59,396,374-59,396,459

128

35

S8

1TGTGAGGGACCTTGTTACTGGGCAG

CATCAGGAGGTGTACTGCCGTACCATA2

chr5:131,658,970-131,659,067

140

46

S9

1CCGAGAGTGGGAGCTACTCATTTTGAGG

CCCTTTAATTAAAGTCGCAGGCACCTAGG2

chrX:153,252,787-153,252,889

145

46

S10

1CTCTGACGTAGTGTGACCTTGCTCATCC

CGAATTCAGCTCTGCTAGGACTGTTGG2

chr5:131,657,322-131,657,462

183

86

S11

1GCTCTTTGCATCGCTCTCTGTCGG

CGTCTTCGCACTTACGCGGAGCGGTAA2

chr21:33,066,198-33,066,362

207

114

 

1=GGGTTCCCTAAGGGTTGGA

2=TCTAGATTGGATCTTGCTGGC

   
  1. N(n): non-sensitive, S(n): sensitive probes for HeLa cells according to data published by the ENCODE consortium. The genomic coordinates are from the human genome assembly of June 2006 (hg18).
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BMC Genomics

ISSN: 1471-2164

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