Noi/NOTES/2014-9-5

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MONOD V5 set A + CRC BSPP capture of tumor DNA samples[edit]

  • Conditions:
    • Probe set: MONOPD V5 set A + CRC from Illumina
    • Probe:target ratio: 200:1
    • Sample: bisDNA and WGBS libraires

MORE DETAILS WILL BE ADDED

Results[edit]

  • For quick test PCR I did qPCR in 10ul reaction with 2ul of circularized DNA and ran for 20 cycles.
  • Loaded 3ul of PCR product to verify the PCR product.

100ng input
File:ZhangLab 2 2014-09-07 20hr 16min 100ng-V5setA-CRC-rep1-gel1.jpg

File:ZhangLab 2 2014-09-07 20hr 16min 100ng-V5setA-CRC-rep1-gel2.jpg
50ng input
File:ZhangLab 2 2014-09-07 20hr 16min 50ng-V5setA-CRC.jpg
200ng input
File:ZhangLab 2 2014-09-07 20hr 16min 200ng-V5setA-CRC.jpg

  • I did qPCR in 100l reaction and purified with 0.7X AMPure beads.
  • Elute with 65l EB buffer
  • Loaded 3ul of sequencing libraries in 6% TBE gel

50ng input
File:ZhangLab 2 2014-09-08 16hr 46min PQ 50ng.jpg
200ng input
File:ZhangLab 2 2014-09-08 16hr 46min PQ 200ng.jpg

2015-03-12[edit]

  • Concentration of sequencing libraries
  • I suggested Alan to pool BSPP capture of 100g bisDNA input Rep 2 for sequencing in March 2015
100ng input Rep1[edit]
Sample Final Conc. (ng/ul) Total volume Yield (ng) Zhang Index Seq(RC)
PCT-1 0.74 60.00 44.39 1 ATCACG
PCT-2 0.93 60.00 55.53 2 CGATGT
PCT-4 0.63 60.00 37.58 3 TTAGGC
PCT-6 0.65 60.00 39.12 4 TGACCA
PCT-7 0.26 60.00 15.76 5 ACAGTG
6T1 0.37 60.00 22.27 6 GCCAAT
6T2 1.32 60.00 79.17 7 CAGATC
6T3 0.50 60.00 29.76 8 ACTTGA
6T4 0.68 60.00 40.68 9 GATCAG
6T5 0.65 60.00 39.26 10 TAGCTT
7T1 1.13 60.00 67.80 11 GGCTAC
7T2 0.26 60.00 15.72 12 CTTGTA
7T3 0.21 60.00 12.42 13 CCATGA
7T4 0.19 60.00 11.18 14 AAGACA
7T5 0.78 60.00 46.65 15 CTTCCT
100ng input Rep2[edit]
Sample Final Conc. (ng/ul) Total volume Yield (ng) Zhang Index Seq(RC)
PCT-1 0.96 60.00 57.38 17 CTCATC
PCT-2 1.46 60.00 87.71 18 AGTTCA
PCT-4 1.10 60.00 65.88 19 GACGCA
PCT-6 0.17 60.00 10.09 20 CCTGTC
PCT-7 0.23 60.00 13.56 21 CAACCC
6T1 0.11 60.00 6.80 22 CTCGGA
6T2 1.97 60.00 118.12 23 TCGAAA
6T3 0.58 60.00 34.89 24 ATTCGC
6T4 1.38 60.00 82.87 25 TACTGC
6T5 0.97 60.00 58.40 26 TCGTGA
7T1 1.28 60.00 76.96 27 TACGCG
7T2 0.87 60.00 52.06 28 AGGTGC
7T3 0.59 60.00 35.70 29 ACGAAC
7T4 2.17 60.00 130.30 30 TTAGTG
7T5 2.14 60.00 128.26 31 CACCAC