Matt:LabNotes/2015-1-21: Difference between revisions
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===Probes, Target and Ampligase Buffer Mix=== | ===Probes, Target and Ampligase Buffer Mix=== | ||
*gDNA: 12878 ( | *gDNA: 12878 (80.3ng/ul) | ||
*[[Matt:LabNotes/2015-1-12 | First strand cDNA from UHRR]] | *[[Matt:LabNotes/2015-1-12 | First strand cDNA from UHRR]] | ||
*[[Matt:LabNotes/2014-11-19#Final_Probes_to_Order:_Trim_to_12.2C000_probes | CA12k_Nov2014 Probes]] | *[[Matt:LabNotes/2014-11-19#Final_Probes_to_Order:_Trim_to_12.2C000_probes | CA12k_Nov2014 Probes]] | ||
**[[Matt:LabNotes/2015-1-5#TBU_Gel_Quantification | V4 (10.7 ng/ul)]] | **[[Matt:LabNotes/2015-1-5#TBU_Gel_Quantification | V4 (10.7 ng/ul)]] | ||
**[[Matt:LabNotes/2015-1-15#TBU_Gel_Quantification | V7 (39.2 ng/ul)]] | **[[Matt:LabNotes/2015-1-15#TBU_Gel_Quantification | V7 (39.2 ng/ul)]] | ||
***Dilute | ***Dilute 2ul into 4ul for easier more accurate pipetting | ||
{| {{table}} | {| {{table}} | ||
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| 2||V4 - cDNA||2.5||3.8||3||20.7||30 | | 2||V4 - cDNA||2.5||3.8||3||20.7||30 | ||
|- | |- | ||
| 3|| | | 3||V4 - NTC||2.5||0||3||24.5||30 | ||
|- | |- | ||
| 4||V7 - cDNA||1||15||3||11||30 | | 4||V7 - gDNA||1||15||3||11||30 | ||
|- | |||
| 5||V7 - cDNA||1||15||3||11||30 | |||
|- | |||
| 6||V7 - NTC||1||0||3||26||30 | |||
|} | |} | ||
Revision as of 01:57, 22 January 2015
CA12k_Nov2014 V4 and V7 in vitro Capture
Calculate Probes Needed
V4
Probe:target | 1000:1 | ' |
Probe size | 3514 | probes |
DNA templet | 300 | ng |
gDNA MW | 1.95x10^12 | g/mol |
gDNA (300ng) | 1.5385x10^-19 | mol |
Probe (1000:1) | 1.5385x10^-16 | mol |
Probe MW (3514, 150nt) | 1.71585106x10^8 | g/mol |
Amount Probe req'd | 26.4 | ng |
V7
Probe:target | 1000:1 | ' |
Probe size | 2486 | probes |
DNA templet | 300 | ng |
gDNA MW | 1.95x10^12 | g/mol |
gDNA (300ng) | 1.5385x10^-19 | mol |
Probe (1000:1) | 1.5385x10^-16 | mol |
Probe MW (2486, 150nt) | 1.21388894x10^8 | g/mol |
Amount Probe req'd | 18.7 | ng |
Probes, Target and Ampligase Buffer Mix
- gDNA: 12878 (80.3ng/ul)
- First strand cDNA from UHRR
- CA12k_Nov2014 Probes
- V4 (10.7 ng/ul)
- V7 (39.2 ng/ul)
- Dilute 2ul into 4ul for easier more accurate pipetting
Sample # | Sample Description | Probes | Target | 10X Ampligase Buffer | H2O | Total |
1 | V4 - gDNA | 2.5 | 3.8 | 3 | 20.7 | 30 |
2 | V4 - cDNA | 2.5 | 3.8 | 3 | 20.7 | 30 |
3 | V4 - NTC | 2.5 | 0 | 3 | 24.5 | 30 |
4 | V7 - gDNA | 1 | 15 | 3 | 11 | 30 |
5 | V7 - cDNA | 1 | 15 | 3 | 11 | 30 |
6 | V7 - NTC | 1 | 0 | 3 | 26 | 30 |
Program
- 95C 30sec -> cool down to 55 C at 0.02C/sec -> 55 C 20h
- -> add 3ul AmpLigase enzyme mix (0.5U/ul AmpLigase in 1X AmpLigase buffer)
- -> 55 C 20h-> 94C 2min -> add 2ul Exo I/III mix-> 37C 2h -> 94C 2min -> 4C hold.