Rui:LabNotes/Haplotyping/2014-12-2: Difference between revisions

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>RuiLiu
(Created page with "==Purpose== * repeat selector procedure: :* selector : gDNA = 200:1; linker : selector = 3:1 :* direct gDNA input: 12, 24, 48ng :* compare selector vs padlock probe :* premade")
 
>RuiLiu
Line 5: Line 5:
:* compare selector vs padlock probe
:* compare selector vs padlock probe
:* premade
:* premade
==Samples==
* HapMap gDNA from Coriell GM18506 (diluted to 50ng/ul)
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8<\hiddentext>
|- style="background-color:#CCFFCC;font-size:10pt"  valign="bottom"
| align="center" width="77" height="15" | &nbsp;
| width="192" | gDNA input
| width="72" | Selector set
| width="72" | Probe ratio
| width="79" | Indx
| width="79" | Test
|- style="font-size:10pt"
| height="15"  valign="bottom" | #1
|  valign="bottom" | 48ng
|  valign="bottom" | linkerV2_UMI
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx01
|  valign="bottom" | selector_UMI
|- style="font-size:10pt"
| height="15"  valign="bottom" | #2
|  valign="bottom" | 24ng
|  valign="bottom" | linkerV2_UMI
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx02
|  valign="bottom" | selector_UMI
|- style="font-size:10pt"
| height="15"  valign="bottom" | #3
|  valign="bottom" | 12ng
|  valign="bottom" | linkerV2_UMI
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx03
|  valign="bottom" | selector_UMI
|- style="font-size:10pt"
| height="15"  valign="bottom" | #4
|  valign="bottom" | NTC
|  valign="bottom" | linkerV2_UMI
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx04
|  valign="bottom" | selector_UMI
|- style="font-size:10pt"
| height="15"  valign="bottom" | #5
|  valign="bottom" | 48ng
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx05
|  valign="bottom" | selector
|- style="font-size:10pt"
| height="15"  valign="bottom" | #6
|  valign="bottom" | 24ng
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx06
|  valign="bottom" | selector
|- style="font-size:10pt"
| height="15"  valign="bottom" | #7
|  valign="bottom" | 12ng
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx07
|  valign="bottom" | selector
|- style="font-size:10pt"
| height="15"  valign="bottom" | #8
|  valign="bottom" | NTC
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx08
|  valign="bottom" | selector
|- style="font-size:10pt"
| height="15"  valign="bottom" | #9
|  valign="bottom" | 48ng
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1
|  valign="bottom" | Indx09
|  valign="bottom" | padlock probe
|- style="font-size:10pt"
| height="15"  valign="bottom" | #10
|  valign="bottom" | 24ng
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1
|  valign="bottom" | Indx10
|  valign="bottom" | padlock probe
|- style="font-size:10pt"
| height="15"  valign="bottom" | #11
|  valign="bottom" | 12ng
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1
|  valign="bottom" | Indx11
|  valign="bottom" | padlock probe
|- style="font-size:10pt"
| height="15"  valign="bottom" | #12
|  valign="bottom" | NTC
|  valign="bottom" | linkerV2
| align="center" valign="bottom" | 200:1
|  valign="bottom" | Indx12
|  valign="bottom" | padlock probe
|- style="font-size:10pt"
| height="15"  valign="bottom" | #13
|  valign="bottom" | 50ng_digested (Kun's, asPC)
|  valign="bottom" | linkerV2_UMI
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx13
|  valign="bottom" | selector_UMI
|- style="font-size:10pt"
| height="15"  valign="bottom" | #14
|  valign="bottom" | 20ng_digested (Kun's, asPC)
|  valign="bottom" | linkerV2_UMI
| align="center" valign="bottom" | 200:1; 3:1
|  valign="bottom" | Indx14
|  valign="bottom" | selector_UMI
|}
==Procedure==
* 1a. R.E digestion

Revision as of 08:28, 4 December 2014

Purpose

  • repeat selector procedure:
  • selector : gDNA = 200:1; linker : selector = 3:1
  • direct gDNA input: 12, 24, 48ng
  • compare selector vs padlock probe
  • premade

Samples

  • HapMap gDNA from Coriell GM18506 (diluted to 50ng/ul)
  gDNA input Selector set Probe ratio Indx Test
#1 48ng linkerV2_UMI 200:1; 3:1 Indx01 selector_UMI
#2 24ng linkerV2_UMI 200:1; 3:1 Indx02 selector_UMI
#3 12ng linkerV2_UMI 200:1; 3:1 Indx03 selector_UMI
#4 NTC linkerV2_UMI 200:1; 3:1 Indx04 selector_UMI
#5 48ng linkerV2 200:1; 3:1 Indx05 selector
#6 24ng linkerV2 200:1; 3:1 Indx06 selector
#7 12ng linkerV2 200:1; 3:1 Indx07 selector
#8 NTC linkerV2 200:1; 3:1 Indx08 selector
#9 48ng linkerV2 200:1 Indx09 padlock probe
#10 24ng linkerV2 200:1 Indx10 padlock probe
#11 12ng linkerV2 200:1 Indx11 padlock probe
#12 NTC linkerV2 200:1 Indx12 padlock probe
#13 50ng_digested (Kun's, asPC) linkerV2_UMI 200:1; 3:1 Indx13 selector_UMI
#14 20ng_digested (Kun's, asPC) linkerV2_UMI 200:1; 3:1 Indx14 selector_UMI

Procedure

  • 1a. R.E digestion