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 m (→Purpose) |
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:* 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" | | |||
| 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