Noi/NOTES/2014-12-8: Difference between revisions

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(Created page with "= LMS + CRC BSPP capture on WGBS libraries prepared from ctDAN of CRC patient (Illumina) = '''Back to calendar'''<br> [[Noi/NOTES/2014-12-5|'''Co...")
 
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** Sample: WGBS libraries prepared by KAPA Hyper Prep Kit (2014-12-05) amount 400ng
** Sample: WGBS libraries prepared by KAPA Hyper Prep Kit (2014-12-05) amount 400ng
==== Probe calculation (Example) ====
==== Probe calculation (Example) ====
'''Probe set         Probe size Probe:target ratio'''
LMS                    73,574               200:1
CRC                 1,024               500:1
<br>
{| {{table}}
| align="center" style="width:220px;background:#f0f0f0;"|'''Probe:target'''
| align="center" style="width:120px;background:#f0f0f0;"|'''200:1'''
| align="center" style="background:#f0f0f0;"|''''''
|-
| 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
|}

Revision as of 21:32, 10 December 2014

LMS + CRC BSPP capture on WGBS libraries prepared from ctDAN of CRC patient (Illumina)

Back to calendar
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