Matt:LabNotes/2013-6-4: Difference between revisions
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>Mzcai (Created page with "Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-22 ===Probe Capture=== *Use the ~37.4 pmole of probes from [http://genome-tech.ucsd.edu/La...") |
>Mzcai No edit summary |
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===Probe Capture=== | ===Probe Capture=== | ||
* | *From [http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-22] and [http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-29]: ~37.4 pmol in 140ul | ||
*Use gDNA as template/target | *Use gDNA as template/target | ||
*Use a probe:target ratio of 100:1 | *Use a probe:target ratio of 100:1 | ||
*Hosuk said there are about 3,000 cells per dish, I will round up to 10,000 so there are extra oligos for multiple experiments | |||
10^4 cells x 10^4 rolonies/cell = 10^8 rolonies in dish <br> | |||
10^8 rolonies / 4,000 genes = 2.5 x 10^4 rolonies/gene (targets) <br> | |||
100 x 2.5 x 10^4 = 2.5 x 10^6 probe sets => 4.151 x 10^-18 mol of probe sets | |||
====100:1 Probe:Target Calculations==== | |||
{| {{table}} | |||
| Probe set size||12964||probes | |||
|- | |||
| gDNA template||300||ng | |||
|- | |||
| gDNA MW||1.95E+12||g/mol (3x10^9 bp x 650 Da/bp + 157.9 Da) | |||
|- | |||
| template||1.5385E-19||mol | |||
|- | |||
| probe sets (100:1)||1.5385E-17||mol | |||
|- | |||
| probe MW (12,964 probes, 193nt)||814190000||g/mol (12,964 probes x (193 nt/probe x 325 Da/nt + 79 Da)) | |||
|- | |||
| amount probe required||1.25263E-08||g | |||
|- | |||
| ||12.5||ng | |||
|- | |||
| | |||
|} |
Revision as of 00:36, 5 June 2013
Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-22
Probe Capture
- Hosuk said there are about 3,000 cells per dish, I will round up to 10,000 so there are extra oligos for multiple experiments
10^4 cells x 10^4 rolonies/cell = 10^8 rolonies in dish
10^8 rolonies / 4,000 genes = 2.5 x 10^4 rolonies/gene (targets)
100 x 2.5 x 10^4 = 2.5 x 10^6 probe sets => 4.151 x 10^-18 mol of probe sets
100:1 Probe:Target Calculations
Probe set size | 12964 | probes |
gDNA template | 300 | ng |
gDNA MW | 1.95E+12 | g/mol (3x10^9 bp x 650 Da/bp + 157.9 Da) |
template | 1.5385E-19 | mol |
probe sets (100:1) | 1.5385E-17 | mol |
probe MW (12,964 probes, 193nt) | 814190000 | g/mol (12,964 probes x (193 nt/probe x 325 Da/nt + 79 Da)) |
amount probe required | 1.25263E-08 | g |
12.5 | ng | |