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

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.
  1. Cosmic3760 0189191
  2. 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

USER-Lig