Kun Zhang LabNote CpG 2007 Oct wk2: Difference between revisions

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(New page: ==Friday 2007-10-12== ===Fri.Exp.Design: Design padlock probes to capture CpG islands=== I'm starting from the primers used in Taylor et al. Cancer Research, 2007, 67:8511-8. To convert th...)
 
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*Convert the right primers to their reverse complementary sequences, add Gs to the end so that the total length of the forward and reverse sequences are the same for all targets;
*Convert the right primers to their reverse complementary sequences, add Gs to the end so that the total length of the forward and reverse sequences are the same for all targets;
*Add common linkers to the two capturing arms.  
*Add common linkers to the two capturing arms.  
*[[Media:PMID17875690_supp_table3.xls | Starting primer file.]]
*It turned out that the padlock probes are pretty long, getting 24 probes cost > $1000. Decided to make 10 shorter ones only. I also manually remove 4 bps from the  PCDGHA12 primers to make them shorter.
*[[Media:PMID17875690_supp_table3.xls | Starting primer file]] and [[Media: PMID17875690_CpG_primers.txt| the actual input file.]]
*[[Media:CpG_primer2padlock.txt | Perl script to convert primers to padlocks.]]
*[[Media:CpG_primer2padlock.txt | Perl script to convert primers to padlocks.]]
*[[Mecia:CpG_padlock_set1.txt | The first set of padlock probes.]]
*[[Mecia:CpG_padlock_set1.txt | The first set of padlock probes.]]

Latest revision as of 08:02, 13 October 2007

Friday 2007-10-12[edit]

Fri.Exp.Design: Design padlock probes to capture CpG islands[edit]

I'm starting from the primers used in Taylor et al. Cancer Research, 2007, 67:8511-8. To convert these sequencing into padlock probes, I need to do the followning: