Noi/NOTES/2014-8-13: Difference between revisions

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>Noi
(Created page with "* noi:DMR220k_LabNotes * 2014-08-13: Received MOMOD V4 Oligo pool from CustomAraay === Oligo info. === * Name: 90K_ologos_04Aug2014 * Conc. 20.53ng/ul, vol. 80ul, amount 1...")
 
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* [[noi:DMR220k_LabNotes]]
= Expansion PCR of new probe set from CustomArrays (90K_ologos_04Aug2014) =
* 2014-08-13: Received MOMOD V4 Oligo pool from CustomAraay
* [[noi:DMR220k_LabNotes| '''Link to calendar''']]
* 2014-08-13: Received MOMOD V4 Oligo (Dr. Zhang recently called V5) pool from CustomAraay
=== Oligo info. ===
=== Oligo info. ===
* Name: 90K_ologos_04Aug2014
* Name: 90K_ologos_04Aug2014
* Conc. 20.53ng/ul, vol. 80ul, amount 1.64ug
* Conc. 20.53ng/ul,  
* Volume 80ul in TE buffer. Total amount 1.64ug
* Info from Dr. Zhang's note
* Info from Dr. Zhang's note
             Description              # oligos  Length      Amp. Primers          Adaptor Removal
             Description              # oligos  Length      Amp. Primers          Adaptor Removal
Line 11: Line 13:
   Total:                              89,107
   Total:                              89,107


* will be working on 73K probe set
* I will be working on 73K probe set
* Length 148 mer (MW = 148 * 330Da/bp =  48,840 Da or g/mole
* Conc. 20.53ng/ul = 420.35nM (20.53ng/ul/ 48,840g/mole)
== Expansion PCR ==
 
 
95C 30sec -> (95C 30sec -> 54C 45sec-> 72C 45sec) X 16-> 72C 3min -> 15C hold<br>
 
:'''-There is something wrong with the oligo pool since I can not amplify all the three subsets of the probes, but it worked for positive control of the three subsets.'''
:'''-We will get CustomArray to re-synthesize the probes'''

Latest revision as of 17:02, 24 December 2014

Expansion PCR of new probe set from CustomArrays (90K_ologos_04Aug2014)[edit]

  • Link to calendar
  • 2014-08-13: Received MOMOD V4 Oligo (Dr. Zhang recently called V5) pool from CustomAraay

Oligo info.[edit]

  • Name: 90K_ologos_04Aug2014
  • Conc. 20.53ng/ul,
  • Volume 80ul in TE buffer. Total amount 1.64ug
  • Info from Dr. Zhang's note
           Description               # oligos   Length      Amp. Primers          Adaptor Removal
  Set A:   BSPP LMS cluster probes    73,574     148nt          V6                   USER/DpnII
  Set B:   Selector LMS cluster       12,994     148nt          V4                   USER/DpnII
  Set C:   Selector chr21 unique       2,539     148nt      eMIP_CA_F/R          Nt.AlwI/Nb.BrsDI
  Total:                              89,107
  • I will be working on 73K probe set
  • Length 148 mer (MW = 148 * 330Da/bp = 48,840 Da or g/mole
  • Conc. 20.53ng/ul = 420.35nM (20.53ng/ul/ 48,840g/mole)

Expansion PCR[edit]

95C 30sec -> (95C 30sec -> 54C 45sec-> 72C 45sec) X 16-> 72C 3min -> 15C hold

-There is something wrong with the oligo pool since I can not amplify all the three subsets of the probes, but it worked for positive control of the three subsets.
-We will get CustomArray to re-synthesize the probes