Dinh:LAB/Bisulfite Sequencing: Difference between revisions
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=Library Contruction= | =Library Contruction= | ||
General protocol: NEBNext(TM) DNA Sample Prep Master Mix Set 1 [[Dinh:LAB/LibraryConstructionProtocol]] | General protocol: NEBNext(TM) DNA Sample Prep Master Mix Set 1 [[Dinh:LAB/LibraryConstructionProtocol]] | ||
=Data Analysis= | |||
==Harvard PD Data== | |||
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-2-26 Feb 26 2010] | |||
=Notebook= | =Notebook= |
Revision as of 23:37, 26 February 2010
Probes Preparation
CpG30K
- 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 CpG30K Probes Set 30ng/ul x 80 ul, purified from 3 plates amplified using EconoTaq (20cycles).
CpG97K
| Jan 24 2009 CpG97K B, 65ulx 15ng/ul
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
- 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 (samples 10-19), 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
- 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.
Library Contruction
General protocol: NEBNext(TM) DNA Sample Prep Master Mix Set 1 Dinh:LAB/LibraryConstructionProtocol
Data Analysis
Harvard PD Data
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>