Noi/NOTES/2014-9-5
Jump to navigation
Jump to search
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