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Table 2 Primer used for analysis of site-specific ChIP products

From: Site-specific chromatin immunoprecipitation: a selective method to individually analyze neighboring transcription factor binding sites in vivo

PCR approach

Target

Primer assay

Sequence

 

Sp1 binding site a

Sp1-a

For: 5'-GCACAGATTTGGCTCGACCTGGA-3'

Rev: 5'-GAGCGGGTGCCCTGAGGAGTTAATT-3'

TFBS specific

Sp1 binding site b

Sp1-b

For: 5'-TGGCCTTGGGTCCCCGCT-3'

Rev: 5'- AGGGCGGGAGGAGGAGGGAC-3

PCR

Sp1 binding site c

Sp1-c

For: 5'-TAGACGTCCGGGCAGCCCCC-3'

Rev: 5'-TCGGGACTCCGGCCGCCT-3'

 

Sp1 binding site d

Sp1-d

For: 5'-AGACCGGACGACAGGCCACCT-3'

Rev: 5'-TCCCGATCAATACTGGACGGAGTCAG-3'

 

RsaI cutting site

RsaI

For: 5'-TGCCATTATCCGACGCTGGCTCTA-3'

Rev: 5'-GAGCGGGTGCCCTGAGGAGTTAATT-3'

 

BfaI cutting site

BfaI

For: 5'-GCACAGATTTGGCTCGACCTGGA-3'

Rev: 5'-AGGGCGGGAGGAGGAGGGAC-3'

enzyme digestion

BfaI 2nd cutting site

BfaI 2

For: 5'-TGGCCTTGGGTCCCCGCT-3'

Rev: 5'-CTTGGGTCCCCGCTGCTGGTT-3'

control

BfaI 3rd cutting site

BfaI 3

For: 5'-TAGACGTCCGGGCAGCCCCC-3'

Rev: 5'-GGTGGCCTGTCGTCCGGTCTG-3'

 

SacI cutting site

SacI

For: 5'-AGACCGGACGACAGGCCACCT-3'

Rev: 5'-CTTTTCCTCCAGAGCCCGACTCG-3'

ChIP control

GAPDH unrelated region

GAPDH

For: 5'-GAGGAAGAGAGAGACCCTCACTG-3'

Rev: 5'-AGGGGTCTACATGGCAACTG-3'