Dinh:LAB/Bisulfite Sequencing: Difference between revisions
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* Breast Cancer Patient Sample (1-9), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-8 DNeasy Blood & Tissue Kit] | * Breast Cancer Patient Sample (1-9), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-8 DNeasy Blood & Tissue Kit] | ||
* Breast Cancer Patient Sample (10-19), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-5 DNeasy Blood & Tissue Kit (improved protocol)] | * Breast Cancer Patient Sample (10-19), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-5 DNeasy Blood & Tissue Kit (improved protocol)] | ||
* Breast Cancer Patient Sample (1-11, 20-28), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-10 DNeasy Blood & Tissue Kit] | |||
=Bisulfite Conversion and Capturing= | =Bisulfite Conversion and Capturing= | ||
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* 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 (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 (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]] | |||
=Notebook= | =Notebook= |
Revision as of 18:49, 14 January 2010
Probes Preparation
- Sep 28 2009 Practice Probes Preparation, CpG30K, 24rxns, Nanodrop: 4.64 ug, End Point Gel Quantification: 1.91 ug
- Oct 1 2009 Probes Preparation, CpG30K, 24rxns, Nanodrop:, End Point Gel Quantification: Problem with 2D gel
- Oct 6 2009 Probes Preparation, CpG30K, 96rxns x 3, Nanodrop: 22.2 ug (last plate: Master Cycler), 55.5 ug (RT-BioRad), 51.5 ug (BioRad). End Point Gel Quantification: 13ng/ul x 46ul
- Oct 27 2009 Probes Preparation, CpG30K, 96rxns, Nanodrop: 67.12 ng/ul (32.2 ug). End Point Gel Quantification: 12ng/ul x 20ul
- Nov 2 2009 Probes Preparation, CpG30K, 96rxns, Nanodrop: 115ng/ul (57.5 ug). End Point Gel Quantification: 7ng/ul x 11ul
- Nov 6 2009 Probes Preparation, CpG30K, 96rxns, Nanodrop: 120ng/ul (60.0 ug). End Point Gel Quantification: 12ng/ul x 22ul
- Nov 17 2009 Probes Preparation, CpG30K, 3 plates of 96rxns, Taq2xMM from NEB, Nanodrop: 100ng/ul (72ug).
- Nov 24 2009 Probes Preparation, CpG30K, KAPA qPCR kit from KAPA Biosystems, Nanodrop: 21.4 ug, End point QUBIT: 23ng/ul x 20 ul
- Dec 30 Probes Set 30ng/ul x 80 ul, purified from 3 plates amplified using EconoTaq (20cycles).
DNA Extraction
- Practice on fibroblast cells culture in suspension AllPrep DNA/RNAeasy Kit
- Breast Cancer Patient Sample (1-9), DNeasy Blood & Tissue Kit
- Breast Cancer Patient Sample (10-19), DNeasy Blood & Tissue Kit (improved protocol)
- Breast Cancer Patient Sample (1-11, 20-28), DNeasy Blood & Tissue Kit
Bisulfite Conversion and Capturing
- Nov 13 2009 Capturing - Practice, CpG30K, Positive control: Jurkat, Negative control: RNAse free-ddH20
- Capturing Breast Cancer Patients (9 samples), Dec 9 2009 Capture Reaction, Dec 15 2009 E-Gel Size selection, Amplification with iProof
- Improving capturing efficiency of CpG30K set for pipelining, Jan 4 2010 Capture Reaction (2pm), Jan 7 2010 Results.
- Breast Cancer patients (10 samples), Jan 6 2010 Bisulfite Conversion, Jan 7 2010 qPCR
- Breast Cancer patients (1-11, 20-28), Jan 12 2010 Bisulfite Conversion, qPCR_of_Bisulfite_Converted_DNA Jan 13 2010
- Breast Cancer Patients (1-28) Samples Track, Dinh:Breast_Cancer_Methylation
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>