Jie:LabNotes/oligo sequences: Difference between revisions

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20080716
  primer to produce spacer:refer to LabNotes on [http://genome-tech.ucsd.edu/LabNotes/index.php/Jie:LabNotes/ExonomeSeq/2008-7-16]
CirclehelperV4_short(20080825):
CirclehelperV4_short(20080825):
   AACAGTGCTCTTCCAGTCTACTAGCCTCATGCGTATCCGATC
   AACAGTGCTCTTCCAGTCTACTAGCCTCATGCGTATCCGATC


AmpFV6.2_2: 5Phos/C*T*GCAGATGTTATCGAGGTC
20080904
AmpRV6.2_2: 5Phos/CTGAATAGGAACGATGAGCC
  Prmer used to amplify the cpg30k and cosmic3760. The amplicon will have 5-terminal phosphate, thus can be ligated after circlehelper insertion.
  AmpFV6.2_2: 5Phos/C*T*GCAGATGTTATCGAGGTC
  AmpRV6.2_2: 5Phos/CTGAATAGGAACGATGAGCC
 
20080918
  confirmation primers for cpg30k. Primers targeting bisulfite conversed DNA to confirm the capture results of cpg30K.
  [[Media: 20080918_conirmed primers for cpg30k.xls]]
 
20080929
  sapcer with length of 60mer that can be ligated without extension.
  Spacer_60mer_reverse: gacctcgataacatctgcagTGCAAAGTAGAACACCAGAACCAGTACAATCACCGTTGCGTTTGGTGAGAATCCTTCCAGCTGAATAGGAACGATGAGCC
  Spacer_60mer: 5’-Phos/ctggaaggattctcaccaaacgcaacggtgattgtactggttctggtgttctactttgca
  [[Media:20080929_spacer of 60mer.doc]]
 
20081019
  confirmation primers for cpg30k from cpg28k library.
  [[Media: 20081019_conirmed primers for cpg30k from cpg28k.xls]]
 
20081019
  positive control used for cosmic probe circlehelper insertion.
  cosmic_probe_control: GTAGACTGGAAGAGCACTGTTGTTGGAGGCTCATCGTTCCTATTCAGCTGCAGATGTTATCGAGGTCCGACGATCGGATACGCATGAGGCTA
 
20081024
  more confirmation primers for cpg30k from cpg28k library.
  [[Media: 20081024_confirmed primers plate_2 for cpg30k from cpg28k.xls]]
  [[Media: 20081024_conirmed primers plate_3 for cpg30k from cpg28k.xls]]

Latest revision as of 22:29, 25 November 2008

20080716

 primer to produce spacer:refer to LabNotes on [1]

CirclehelperV4_short(20080825):

 AACAGTGCTCTTCCAGTCTACTAGCCTCATGCGTATCCGATC

20080904

 Prmer used to amplify the cpg30k and cosmic3760. The amplicon will have 5-terminal phosphate, thus can be ligated after circlehelper insertion.
 AmpFV6.2_2: 5Phos/C*T*GCAGATGTTATCGAGGTC
 AmpRV6.2_2: 5Phos/CTGAATAGGAACGATGAGCC

20080918

 confirmation primers for cpg30k. Primers targeting bisulfite conversed DNA to confirm the capture results of cpg30K.
 Media: 20080918_conirmed primers for cpg30k.xls

20080929

 sapcer with length of 60mer that can be ligated without extension.
 Spacer_60mer_reverse: gacctcgataacatctgcagTGCAAAGTAGAACACCAGAACCAGTACAATCACCGTTGCGTTTGGTGAGAATCCTTCCAGCTGAATAGGAACGATGAGCC
 Spacer_60mer: 5’-Phos/ctggaaggattctcaccaaacgcaacggtgattgtactggttctggtgttctactttgca
 Media:20080929_spacer of 60mer.doc

20081019

 confirmation primers for cpg30k from cpg28k library. 
 Media: 20081019_conirmed primers for cpg30k from cpg28k.xls

20081019

 positive control used for cosmic probe circlehelper insertion.
 cosmic_probe_control: GTAGACTGGAAGAGCACTGTTGTTGGAGGCTCATCGTTCCTATTCAGCTGCAGATGTTATCGAGGTCCGACGATCGGATACGCATGAGGCTA

20081024

 more confirmation primers for cpg30k from cpg28k library. 
 Media: 20081024_confirmed primers plate_2 for cpg30k from cpg28k.xls
 Media: 20081024_conirmed primers plate_3 for cpg30k from cpg28k.xls