Kun:LabNotes/ExonomeSeq: Difference between revisions
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==Probe Design== | ==Probe Design== | ||
*The first probe set: [[Kun:LabNotes/ExonomeSeq/2007-11-15]] | ===Oct08 whole exome probe set=== | ||
*Athurva created a list of non-redundant coding exons for all RefSeq genes. | |||
**[[Media: refExon.txt.gz | Exon Info file]]. | |||
**[[Media: refExonLink.txt.gz | RefSeq vs. Exon link file]]. | |||
*Athurva has converted my Cpg probe design program for exon probe design. He has made a number of changes including the strategy to search for a optimal set of probes for a large exon. I made additional changes on the codes. Here is the [[Media: getExonProbes.txt | current version of probe design program]]. | |||
===The first probe set: [[Kun:LabNotes/ExonomeSeq/2007-11-15]]=== | |||
*One 55k library received on 12/12/2007, OLID: 018274110001, 10pmole, resuspended in 500ul RT-PCR grade water (new vial) -> 20nM x 500ul -> Take 100ul out to a 1.5ml non-stick tube as the working tube. | *One 55k library received on 12/12/2007, OLID: 018274110001, 10pmole, resuspended in 500ul RT-PCR grade water (new vial) -> 20nM x 500ul -> Take 100ul out to a 1.5ml non-stick tube as the working tube. | ||
*The second probe set: [[Kun:LabNotes/ExonomeSeq/2007-12-21]] | *The second probe set: [[Kun:LabNotes/ExonomeSeq/2007-12-21]] | ||
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<b>Received 01/24/2008.</b> | <b>Received 01/24/2008.</b> | ||
10pmole, resuspended in 500ul RT-PCR grade water (new vial) -> 20nM x 500ul -> Take 100ul out to a 1.5ml non-stick tube as the working tube. | 10pmole, resuspended in 500ul RT-PCR grade water (new vial) -> 20nM x 500ul -> Take 100ul out to a 1.5ml non-stick tube as the working tube. | ||
==Overview of experiments== | ==Overview of experiments== | ||
*[[Kun:LabNotes/ExonomeSeq/Overview_121207_020808| Dec-12-07 to Feb-08-08]] | *[[Kun:LabNotes/ExonomeSeq/Overview_121207_020808| Dec-12-07 to Feb-08-08]] |
Revision as of 01:25, 22 October 2008
2008 <calendar> name=Kun:LabNotes/ExonomeSeq format=%name/%year-%month-%day date=2008/02/01 view=oneyear </calendar>
2007 <calendar> name=Kun:LabNotes/ExonomeSeq format=%name/%year-%month-%day date=2007/11/01 view=threemonths </calendar>
Probe Design
Oct08 whole exome probe set
- Athurva created a list of non-redundant coding exons for all RefSeq genes.
- Athurva has converted my Cpg probe design program for exon probe design. He has made a number of changes including the strategy to search for a optimal set of probes for a large exon. I made additional changes on the codes. Here is the current version of probe design program.
The first probe set: Kun:LabNotes/ExonomeSeq/2007-11-15
- One 55k library received on 12/12/2007, OLID: 018274110001, 10pmole, resuspended in 500ul RT-PCR grade water (new vial) -> 20nM x 500ul -> Take 100ul out to a 1.5ml non-stick tube as the working tube.
- The second probe set: Kun:LabNotes/ExonomeSeq/2007-12-21
- Two Agilent 55k libraries were ordered on 01/04/2008.
- Cosmic3760 0189191
- CpgCes: Cpg28k + CES27k 0189181
Received 01/24/2008. 10pmole, resuspended in 500ul RT-PCR grade water (new vial) -> 20nM x 500ul -> Take 100ul out to a 1.5ml non-stick tube as the working tube.
Overview of experiments
Sequencing library construction
Random primed
- Forward primer (SolFN6):CGACGCTCTTCCGATCTNNNNNN Tm left = 59.20C
- Reverse primer (SolRN6):CATACGAGCTCTTCCGATCTNNNNNN Tm left = 59.45C