Kun:LabNotes/ExonomeSeq/2007-12-21: Difference between revisions
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==Probe design Version 2== | ==Probe design Version 2== | ||
I came up with an iterative primer searching program when working on the design of CpG island probes. I decided to modify this program for exonome probe design since it will generate probes for many regions that were missing by Keith's program. Here is the [[Media:getExonicPrimers.txt|code of my program]]. I was able to design | I came up with an iterative primer searching program when working on the design of CpG island probes. I decided to modify this program for exonome probe design since it will generate probes for many regions that were missing by Keith's program. Here is the [[Media:getExonicPrimers.txt|code of my program]]. The gap for fill-ins is ~250bp. I was able to design 381,765 probes covering 183,448 exons in the human RefSeq genes. The total length of exonic sequences captured is 80,719,171bps. The total non-overlapping genomic regions covered by this probe set is 68,730,151bps. I selected a subset of 55,067 probes targeting the first 3760 genes in the Cosmic gene database. The last 67 probes were removed to make a 55k set. This is the second 55k exonic chip synthesized at Agilent, called Cosmic3760 library. I used the V4 adaptors and the V7 linker. The reason of using V4 adaptor is to have the option of using BciVI. | ||
*[[Media: | *[[Media:ECosmic3760_probes.txt|Probe information file.]] | ||
*[[Media: | *[[Media:Cosmic3760.seq|Raw sequences of all 55,000 probes.]] |
Revision as of 07:18, 5 January 2008
Exp. 1 Perform another round of E55kv1 capturing experiment
Shearing template DNA
10ul 353ng/ul GM10835 gDNA + 750ul shearing buffer (1X TE w/ 10% Glycerol) -> sheared with Nebulizer with unknown pressure for 1min -> recovered 650ul -> isopropanol precipitation with the presence of 4ul linear acrylamide.
Resuspended in 10ul ddH2O -> ~300ng/ul
Circularization reaction
Exp.2 Exon capture experiment
Sheared NA10835(~300ng/ul) 3ul E55kv1 probes 107nM 17ul 10X Ampligase buffer 2.25ul
95C 10min -> 60C 40h -> add 2.5ul NSL mix -> 60C 1h -> (95C 2min -> 60C 1h) x 20 -> 37C 1min -> add 2ul exo I&III, 1ul T7 exo -> 37C 2h -> 95C 2min -> 4c hold
Probe design Version 2
I came up with an iterative primer searching program when working on the design of CpG island probes. I decided to modify this program for exonome probe design since it will generate probes for many regions that were missing by Keith's program. Here is the code of my program. The gap for fill-ins is ~250bp. I was able to design 381,765 probes covering 183,448 exons in the human RefSeq genes. The total length of exonic sequences captured is 80,719,171bps. The total non-overlapping genomic regions covered by this probe set is 68,730,151bps. I selected a subset of 55,067 probes targeting the first 3760 genes in the Cosmic gene database. The last 67 probes were removed to make a 55k set. This is the second 55k exonic chip synthesized at Agilent, called Cosmic3760 library. I used the V4 adaptors and the V7 linker. The reason of using V4 adaptor is to have the option of using BciVI.