Dinh:LAB/Bisulfite Sequencing: Difference between revisions

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* 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.
* 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.
== SALK Institute: Methylation of HGPS fibroblasts, Dr. Guanghui Liu ==
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-3-8 March 8-11 2010]. Samples sent to Harvard for shearing 3/11/10.


=Library Contruction=
=Library Contruction=

Revision as of 17:21, 15 March 2010

Probes Preparation

CpG30K

CpG97K

| Jan 24 2009 CpG97K B, 65ulx 15ng/ul

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
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. 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
  • Capture PCR Reaction with AmpF/R6.3NH2, CpG97K A/B. Template: 10-15. Jan 25 2010, size selection Jan 26 2010, Re-Amplification 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. Feb 8 2010, size selection Feb 12 2010, capture amplification with leftover product Feb 17 2010. E-gel size selection by Ida & samples sent to Harvard for Covaris shearing (all 100bp fragments), Feb 17 2010.

SALK Institute: Methylation of HGPS fibroblasts, Dr. Guanghui Liu

March 8-11 2010. Samples sent to Harvard for shearing 3/11/10.

Library Contruction

General protocol: NEBNext(TM) DNA Sample Prep Master Mix Set 1 Dinh:LAB/LibraryConstructionProtocol

Data Analysis

Harvard PD Data

Feb 26 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>