Noi/NOTES/2014-12-8
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LMS + CRC BSPP capture on WGBS libraries prepared from ctDAN of CRC patient (Illumina)
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Continued from 2014-12-05
- Conditions:
- Probe set: MONOPD V5 set A (LMS) + CRC from Illumina
- Probe:target ratio: 200:1 for LMS probe set, 500:1 for CRC probe set from Illumina
- Sample: WGBS libraries prepared by KAPA Hyper Prep Kit (2014-12-05) amount 400ng
Probe calculation (Example)
Probe set Probe size Probe:target ratio LMS 73,574 200:1 CRC 1,024 500:1
Probe:target | 200:1 | ' |
Probe size | 73574 | |
Template | 400 | ng |
Human gDNA MW | 1.95E+12 | g/mol (3E+09 * 650Da/bp+157.9Da) |
Human gDNA (400ng) | 2.05128E-19 | mol (400ng/1.9500E+12 g/mol) |
Probe required (200:1) | 4.10256E-17 | mol (2.5641E-20 * 200) |
Probe MW (73,574 probes, 110nt) | 2.636E+09 | g/mol (73,574 probes * (110nt * 325Da/nt + 79Da)) |
Amount probe required | 1.081E-07 | g (2.051E-17mol * 2.636E+09g/mol) |
Amount probe required | 108 | ng |
CRC required (200:1) | 1.50 | ng |
CRC required (500:1) | 3.76 | ng |
CRC conc. | 13.2 | ng/ul |