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* [[Dinh:Protocols/Capturing_Nov13| Nov 13 2009 Capturing - Practice]], CpG30K, Positive control: Jurkat, Negative control: RNAse free-ddH20 * Improving capturing efficiency of CpG30K set for pipelining, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-4 Jan 4 2010] Capture Reaction (2pm), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-7#RT_PCR_of_Capture_Products_.28optimization.29 Jan 7 2010] Results. ==Breast Cancer Patients, Diet and Methylation Study== * Capturing Breast Cancer Patients (samples 1-9), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-9 Dec 9 2009] Capture Reaction, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-15 Dec 15 2009] E-Gel Size selection, Amplification with iProof * Breast Cancer patients (samples 10-19), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-6 Jan 6 2010] Bisulfite Conversion, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-7#RT_PCR_of_Bisulfite_Converted_DNA Jan 7 2010] qPCR * Breast Cancer patients (1-11, 20-28), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-12 Jan 12 2010] Bisulfite Conversion, [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-13 qPCR_of_Bisulfite_Converted_DNA Jan 13 2010] Breast Cancer Patients (1-28) Samples Track, [[Dinh:Breast_Cancer_Methylation]] * Capturing Test, CpG97A/B. Templates: bis_Jurkat, bis_16. Conditions: 55C vs 60C, 0 Cycling. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-11 Jan 10 2010] * Capture, CpG97A/B. Templates: bis_10-14, bis_Jurkat. Condition: 55C, 0 Cycling. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-15 Jan 15 2010] * Capture Re-test for Sanger Sequencing, CpG97A/B. Template: bis_15. Condition: 55C vs 60C, 0 Cycling. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-21 Jan 21 2010] * Capture PCR Reaction with AmpF/R6.3NH2, CpG97K A/B. Template: 10-15. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-25 Jan 25 2010], size selection [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-26 Jan 26 2010], Re-Amplification [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-27 Jan 27 2010], Samples sent to Illumina for Covaris shearing (all 100bp fragments) Jan 29 2010. * Capture PCR Reaction with AmpF/R6.3NH2, CpG97A/B. Template: bis_16-28, jurkat. Condition: 55C annealing temp. 0 Cycling. [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-2-8 Feb 8 2010], size selection [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-2-12 Feb 12 2010], capture amplification with leftover product [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-2-17 Feb 17 2010]. E-gel size selection by Ida & samples sent to Harvard for Covaris shearing (all 100bp fragments), Feb 17 2010.
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