Dinh:LAB/Bisulfite Sequencing: Difference between revisions

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=Probes Preparation=
* [[Dinh:Protocols/Probes_Prep | Probes Preparation]]
* [[Dinh:Protocols/Probes_Prep_Sep28|Sep 28 2009 Practice Probes Preparation]], CpG30K, 24rxns, Nanodrop: 4.64 ug, End Point Gel Quantification: 1.91 ug
* [[Dinh:Protocols/DNA_Extraction | DNA Extraction]]
* [[Dinh:Protocols/Probes_Prep_Oct1| Oct 1 2009 Probes Preparation]], CpG30K, 24rxns, Nanodrop:, End Point Gel Quantification: Problem with 2D gel
* [[Dinh:Protocols/Bisulfite_Capture | Bisulfite Capture]]
* [[Dinh:Protocols/Probes_Prep_Oct6| 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
* [[Dinh:Sample_Tracker | Sample Tracking Information]]
* [[Dinh:Protocols/Probes_Prep_Oct27| Oct 27 2009 Probes Preparation]], CpG30K, 96rxns, Nanodrop: 67.12 ng/ul (32.2 ug). End Point Gel Quantification: 12ng/ul x 20ul
* [[Dinh:Protocols/Probes_Prep_Nov2| Nov 2 2009 Probes Preparation]], CpG30K, 96rxns, Nanodrop: 115ng/ul (57.5 ug). End Point Gel Quantification: 7ng/ul x 11ul
* [[Dinh:Protocols/Probes_Prep_Nov6| Nov 6 2009 Probes Preparation]], CpG30K, 96rxns, Nanodrop: 120ng/ul (60.0 ug). End Point Gel Quantification: 12ng/ul x 22ul


*[[Dinh:Protocols/Probes_Prep_Nov17| Nov 17 2009 Probes Preparation]], CpG30K, 3 plates of 96rxns, Taq2xMM from NEB, Nanodrop: 100ng/ul (72ug).
=Notebook=
 
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*[[Dinh:Protocols/Probes_Prep_Nov24| Nov 24 2009 Probes Preparation]], CpG30K, KAPA qPCR kit from KAPA Biosystems, Nanodrop: 21.4 ug, End point [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-4 QUBIT]: 23ng/ul x 20 ul
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*[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-29 Dec 30 Probes Set] 30ng/ul x 80 ul, purified from 3 plates amplified using EconoTaq (20cycles).
date=2011/07/01
 
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=DNA Extraction=
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* Practice on fibroblast cells culture in suspension [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2009-12-1 AllPrep DNA/RNAeasy 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)]
 
=Bisulfite Conversion and Capturing=
* [[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).
 
* Breast Cancer patients (10 samples), [http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-1-6 Jan 6 2010] Bisulfite Conversion,


=Notebook=
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==John Hopkins U. Tumor Samples==
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-8-22 August 22 2010]. Bisulfite Conversion (8/22)
==Breast Cancer Patients, Diet and Methylation Study==
**BSPP Breast Cancer Data Mapping [http://genome-tech.ucsd.edu/LabNotes/upload/1/19/BSPP_Diet_Cancer_Mapping_%283%29.ods]
== 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.

Latest revision as of 02:24, 19 April 2011

Notebook[edit]

<calendar> name=Dinh format=%name/NOTES/%year-%month-%day date=2011/07/01 view=oneyear </calendar>

<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>

John Hopkins U. Tumor Samples[edit]

August 22 2010. Bisulfite Conversion (8/22)

Breast Cancer Patients, Diet and Methylation Study[edit]

    • BSPP Breast Cancer Data Mapping [1]

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

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