Dinh/Dinh 2014/NOTES/2014-3-12
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Template DNA | Amount (ng) | Probes | Probes to target | Annealing temperature | Polymerase | %Map | %unique | Specificity | Sensitivity | #CpGs(1X) |
GM12878 - 0615 - Phusion Dual | 240 | A-F | 200 | 56.4 | PhusionU+HemoKlentaq | 42% | 99%, 42,815 reads | 79% | 1% | |
GM12878 - 0615 - Phusion Single | 240 | A-F | 200 | 56.4 | PhusionU+HemoKlentaq | 43% | 99%, 42,952 reads | 80% | 1% | |
GM12878 - 0615 - KAPA | 240 | A-F | 200 | 56.4 | PhusionU+HemoKlentaq | 43% | 99%, 99,492 reads | 42% | 1% | 171 |
GM12878 - 0615 - KAPA | 60 | A-F | 200 | 56.4 | HemoKlentaq | 64% | 99%, 82,224 reads | 38% | 1% | 268 |
GM12878 - 0615 - KAPA | 60 | A-F | 200 | 56.4 | HemoKlentaq | 65% | 98%, 94,514 reads | 39% | 1% | 410 |
GM12878 - 0615 - KAPA | 60 | A-F | 200 | 56.4 | PfuTurboCX | 62% | 57%, 153,821 reads | 61% | 1% | 1347 |
GM12878 - 0615 - KAPA | 60 | A-F | 200 | 56.4 | PhusionU | 72% | 76%, 165,924 reads | 70% | 2% | 3421 |
GM12878 - 0615 - KAPA | 60 | A-F | 200 | 56.4 | PhusionU | 69% | 84%, 173,935 reads | 59% | 1% | 3234 |
H1 p54 - Ctrl TeSR | 193.9 | A-F | 100 | 55 | HemoKlentaq | NA | NA | NA | NA | NA |
H1 p54 - Activin-A | 362 | A-F | 100 | 55 | HemoKlentaq | NA | NA | NA | NA | NA |
H1 p47 - Ctrl TeSR | 144.95 | A-F | 100 | 55 | HemoKlentaq | NA | NA | NA | NA | NA |
H1 p47 - BMP-4 | 205.6 | A-F | 100 | 55 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | A | 100 | 55 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | A | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | A | 100 | 58.8 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | A | 100 | 60 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | A | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | B | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | C | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | D | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | E | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 150 | F | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 300 | C | 100 | 56.1 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 300 | C | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 300 | C | 100 | 56.9 | HemoKlentaq | 53% | 98% | 81% | 2% | 63,054 |
GM12878 | 300 | A-F | 100 | 56.4 | HemoKlentaq | 11% | 99% | 68% | 2% | 75,542 |
GM12878 | 300 | A-F | 50 | 56.4 | HemoKlentaq | 36% | 98% | 79% | 3% | 85,528 |
GM12878 | 300 | A-F | 30 | 56.4 | HemoKlentaq | 40% | 95% | 79% | 4% | 113,509 |
GM12878 | 46.5 | A-F | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 93 | A-F | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
GM12878 | 341 | A-F | 100 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
H1 p54 - Ctrl TeSR | 501.6 | A-F | 100 | 56.4 | HemoKlentaq | 37% | 87% | 55% | 15% | NA |
H1 p54 - Activin A | 469.7 | A-F | 100 | 56.4 | HemoKlentaq | 35% | 86% | 53% | 13% | NA |
H1 p47 - Ctrl TeSR | 314.6 | A-F | 100 | 56.4 | HemoKlentaq | 44% | 74% | 56% | 15% | NA |
H1 p47 - BMP-4 | 308 | A-F | 100 | 56.4 | HemoKlentaq | 38% | 80% | 53% | 16% | NA |
hESC - d0 #1 | 465.3 | A-F | 100 | 56.4 | HemoKlentaq | 51% | 65% | 57% | 15% | NA |
hESC - d0 #2 | 482.9 | A-F | 100 | 56.4 | HemoKlentaq | 50% | 66% | 58% | 18% | NA |
hESC - d0 #3 | 409.2 | A-F | 100 | 56.4 | HemoKlentaq | 52% | 73% | 59% | 19% | NA |
DE-d3 #1 | 430.1 | A-F | 100 | 56.4 | HemoKlentaq | 55% | 62% | 60% | 19% | NA |
DE-d3 #2 | 413.6 | A-F | 100 | 56.4 | HemoKlentaq | 34% | 85% | 54% | 13% | NA |
DE-d3 #3 | 376.2 | A-F | 100 | 56.4 | HemoKlentaq | 57% | 61% | 61% | 18% | NA |
naïve ESC #1 | 413.6 | A-F | 100 | 56.4 | HemoKlentaq | 48% | 66% | 50% | 8% | NA |
naïve ESC #2 | 470.8 | A-F | 100 | 56.4 | HemoKlentaq | 53% | 68% | 60% | 18% | NA |
HT1080 | 300 | E | 200 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
HT1080 | 300 | E | 200 | 56.4 | PfuTurboCX | NA | NA | NA | NA | NA |
HT1080 | 300 | E | 200 | 56.4 | Stoffel | NA | NA | NA | NA | NA |
HT1080 | 300 | E | 200 | 56.4 | KlenTherm | NA | NA | NA | NA | NA |
HT1080 | 300 | E | 200 | 56.4 | Truncated Taq | NA | NA | NA | NA | NA |
HT1080 | 300 | E | 200 | 56.4 | No polymerase | NA | NA | NA | NA | NA |
HT1080 | 100 | A | 200 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
HT1080 | 200 | A | 200 | 56.4 | HemoKlentaq | NA | NA | NA | NA | NA |
HT1080 | 100 | A | 200 | 56.4 | KlenTherm | NA | NA | NA | NA | NA |
HT1080 | 200 | A | 200 | 56.4 | KlenTherm | NA | NA | NA | NA | NA |
HT1080 | 100 | A | 200 | 56.4 | No polymerase | NA | NA | NA | NA | NA |
HT1080 | 200 | A | 200 | 56.4 | No polymerase | NA | NA | NA | NA | NA |
HT1080 | 100 | A | 200 | 56.4 | PfuTurboCX | NA | NA | NA | NA | NA |
HT1080 | 200 | A | 200 | 56.4 | PfuTurboCX | NA | NA | NA | NA | NA |
HT1080 | 100 | A | 200 | 56.4 | Stoffel | NA | NA | NA | NA | NA |
HT1080 | 200 | A | 200 | 56.4 | Stoffel | NA | NA | NA | NA | NA |
HT1080 | 100 | A | 200 | 56.4 | Truncated Taq | NA | NA | NA | NA | NA |
HT1080 | 200 | A | 200 | 56.4 | Truncated Taq | NA | NA | NA | NA | NA |