Dinh:LAB/Bisulfite Sequencing: Difference between revisions

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=Bisulfite Conversion and Capturing=
=Bisulfite Conversion and Capturing=
* [[Dinh:Protocols/Capturing_Nov13| Nov 13 2009 Capturing - Practice]], CpG30K, Positive control: Jurkat, Negative control: RNAse free-ddH20
* [[Dinh:Protocols/Capturing_Nov13| Nov 13 2009 Capturing - Practice]], CpG30K, Positive control: Jurkat, Negative control: RNAse free-ddH20
* Capturing Breast Cancer Patients (9 samples), [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


* 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.
* 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 (10 samples), [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, 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 (1-11, 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]]
* 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]


=Notebook=
=Notebook=

Revision as of 18:10, 22 January 2010

Probes Preparation

  • Dec 30 Probes Set 30ng/ul x 80 ul, purified from 3 plates amplified using EconoTaq (20cycles).

DNA Extraction

Bisulfite Conversion and Capturing

  • Improving capturing efficiency of CpG30K set for pipelining, Jan 4 2010 Capture Reaction (2pm), Jan 7 2010 Results.

Breast Cancer Patients, Diet and Methylation Study

  • Capturing Breast Cancer Patients (samples 1-9), Dec 9 2009 Capture Reaction, Dec 15 2009 E-Gel Size selection, Amplification with iProof
  • Capturing Test, CpG97A/B. Templates: bis_Jurkat, bis_16. Conditions: 55C vs 60C, 0 Cycling. Jan 10 2010
  • Capture, CpG97A/B. Templates: bis_10-14, bis_Jurkat. Condition: 55C, 0 Cycling. Jan 15 2010
  • Capture Re-test for Sanger Sequencing, CpG97A/B. Template: bis_15. Condition: 55C vs 60C, 0 Cycling. Jan 21 2010

Notebook

<calendar> name=Dinh format=%name/NOTES/%year-%month-%day date=2010/07/01 view=oneyear </calendar>

<calendar> name=Dinh format=%name/NOTES/%year-%month-%day date=2009/07/01 view=oneyear </calendar>