Rui:LabNotes/Haplotyping/2011-11-3: Difference between revisions

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@27ct, #3,4 start to up [[File:11.3.11_27ct.jpg|400px]] @30ct, all start up [[File:11.3.11_30ct.jpg|400px]]
@27ct, #3,4 start to up [[File:11.3.11_27ct.jpg|400px]] @30ct, all start up [[File:11.3.11_30ct.jpg|400px]]
===EtOH precipitation===
* Samples: 17-2, 22-3, 27-3,4, 30-1,2,3,4
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''ng/ul'''
| align="center" style="background:#f0f0f0;"|'''total (ng)'''
| align="center" style="background:#f0f0f0;"|'''up Ct'''
| align="center" style="background:#f0f0f0;"|'''stop Ct'''
| align="center" style="background:#f0f0f0;"|'''dCt'''
| align="center" style="background:#f0f0f0;"|'''dFlu.'''
|-
| 17-2||6.95||34.75||12||17||5||400
|-
| 22-3||15.1||75.5||12||22||10||500
|-
| 27-3||1.29||6.45||22||26||4||100
|-
| 27-4||1.17||5.85||22||26||4||100
|-
| 30-1||21.5||107.5||20||30||10||300
|-
| 30-2||10.1||50.5||24||30||6||300
|-
| 30-3||15.8||79||20||30||10||400
|-
| 30-4||6.35||31.75||27||30||3||100
|}

Latest revision as of 19:07, 4 November 2011

Test condition for haplotyping[edit]

  • Start with ~1pg cell lysate aliquot
  • Perform limited time MDA
  • Tagmentation and PCR
  • Need to achieve ~1000X increase. Based on 50cell experiments, it seems 1k-2k increase after 2hrs when QPCR shoots up around 12ct and reach the saturation at 20ct.
  • Key point is when to stop MDA based on QPCR curve

Samples[edit]

Procedures[edit]

Results[edit]

Ctrls File:11.3.11 Ctrls.jpg

@17ct, #2 up File:11.3.11 17ct.jpg @22ct, #3 up File:11.3.11 22ct.jpg

@27ct, #3,4 start to up File:11.3.11 27ct.jpg @30ct, all start up File:11.3.11 30ct.jpg


EtOH precipitation[edit]

  • Samples: 17-2, 22-3, 27-3,4, 30-1,2,3,4
' ng/ul total (ng) up Ct stop Ct dCt dFlu.
17-2 6.95 34.75 12 17 5 400
22-3 15.1 75.5 12 22 10 500
27-3 1.29 6.45 22 26 4 100
27-4 1.17 5.85 22 26 4 100
30-1 21.5 107.5 20 30 10 300
30-2 10.1 50.5 24 30 6 300
30-3 15.8 79 20 30 10 400
30-4 6.35 31.75 27 30 3 100