Rui:LabNotes/Haplotyping/2011-11-4: Difference between revisions
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>RuiLiu m (Created page with '==Test condition for haplotyping== * Continue with lab note 11.3.11 * Tagmentation and PCR ===Samples=== * Non-MDA ~1pg cell lysates: from same patch of cells as MDA samples, Pt…') |
>RuiLiu m (→Results) |
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===Results=== | ===Results=== | ||
MDA samples [[File:11.4.11_MDA-nextera.jpg|400px]] non-MDA samples [[File:11.4.11_ctrls.jpg|400px]] | MDA samples [[File:11.4.11_MDA-nextera.jpg|400px]] non-MDA samples [[File:11.4.11_ctrls.jpg|400px]] | ||
gel check: MDA samples are over-amplified except 2 from 27ct[[File:11.4.11_gel.jpg|300px]] | |||
==Simplify protocol== | |||
* Skip purification after MDA | |||
* Combine 2 rounds of PCR | |||
===Samples=== | |||
* 10ng jurkat + 1ul dALS + 1ul dNS + 7ul MDA MM --> take 3ul for tagmentation | |||
* 1ul each of all 8 MDA product [17ct-2, 22ct-3, 27ct-3,4, 30ct-1,2,3,4] ranging from 1ng - 20ng | |||
===Procedure=== | |||
* 3ng jurkat in 10ul MDA MM --> 65C, 3min | |||
* 5ul tagmentation reaction | |||
* 30ul PCR: 15ul Kapa QPCR, 0.6ul Adaptor 1, 0.6ul barcoded-adaptor 2 (GA-A2 Indx73-80) | |||
* 58C, 4 cycles; 62C, 8 cycles | |||
===Results=== | |||
* Consistent with previous curve, suggesting 1 step PCR works | |||
* Jurkat gDNA directly with MDA MM seems fine with tagmentation and PCR, suggesting purification can skip | |||
58C for 4 cycles [[File:11.4.11_58C.jpg|400px]] 62C for 8 cycles [[File:11.4.11_62C.jpg|400px]] | |||
gel check after beads purification [[File:11.7.11_gel.jpg|300px]] |
Latest revision as of 18:30, 7 November 2011
Test condition for haplotyping[edit]
- Continue with lab note 11.3.11
- Tagmentation and PCR
Samples[edit]
- Non-MDA ~1pg cell lysates: from same patch of cells as MDA samples, Ptnase treatment, Nextera
- MDA samples: 1ul each of all 8 MDA product [17ct-2, 22ct-3, 27ct-3,4, 30ct-1,2,3,4] ranging from 1ng - 20ng
Procedure[edit]
- Tagmentation: 1ul 1:50d Trp-I, 1ul LMW buffer, fill up to 5ul
- PCR: 15ul Kapa QPCR MM, 0.3ul each B/O primer, fill up to 30ul
Results[edit]
MDA samples File:11.4.11 MDA-nextera.jpg non-MDA samples File:11.4.11 ctrls.jpg
gel check: MDA samples are over-amplified except 2 from 27ctFile:11.4.11 gel.jpg
Simplify protocol[edit]
- Skip purification after MDA
- Combine 2 rounds of PCR
Samples[edit]
- 10ng jurkat + 1ul dALS + 1ul dNS + 7ul MDA MM --> take 3ul for tagmentation
- 1ul each of all 8 MDA product [17ct-2, 22ct-3, 27ct-3,4, 30ct-1,2,3,4] ranging from 1ng - 20ng
Procedure[edit]
- 3ng jurkat in 10ul MDA MM --> 65C, 3min
- 5ul tagmentation reaction
- 30ul PCR: 15ul Kapa QPCR, 0.6ul Adaptor 1, 0.6ul barcoded-adaptor 2 (GA-A2 Indx73-80)
- 58C, 4 cycles; 62C, 8 cycles
Results[edit]
- Consistent with previous curve, suggesting 1 step PCR works
- Jurkat gDNA directly with MDA MM seems fine with tagmentation and PCR, suggesting purification can skip
58C for 4 cycles File:11.4.11 58C.jpg 62C for 8 cycles File:11.4.11 62C.jpg
gel check after beads purification File:11.7.11 gel.jpg