Noi/NOTES/2014-12-8

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Revision as of 21:32, 10 December 2014 by >Noi
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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