Dinh:Thesis Overview: Difference between revisions

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=Thesis Project Overview=
==Samples: Data analysis ==
==Samples: Data analysis ==
=== Salk's Human Tissues Whole Genome Bisulfite Sequencing ===
* Sample set codes starting with A.
=== A-Salk. Salk's Human Tissues Whole Genome Bisulfite Sequencing ===
* Paper: Not out yet
* Paper: Not out yet
=== Human peripheral mononuclear cells trio - type 2 diabetes - father, mother, daughter===
=== A-BGI. Human peripheral mononuclear cells trio - type 2 diabetes - father, mother, daughter===
** Paper: http://genomebiology.com/2014/15/7/408
** Paper: http://genomebiology.com/2014/15/7/408
* ''' Human whole blood DNA methylation study - newborn, middle-age, centarian'''
=== A-WB. Human whole blood DNA methylation study - newborn, middle-age, centarian===
** Paper: http://www.pnas.org/content/109/26/10522.full
** Paper: http://www.pnas.org/content/109/26/10522.full


===Samples: Data generation ===  
==Samples: Data generation ==
* ''' Early definitive endoderm differentiation (Song's 3-days protocol)'''
* Sample set codes starting with G.
=== G-SS. Early definitive endoderm differentiation (Song's 3-days protocol and Sergio's H1 samples)===
{| class="wikitable"
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Tube ID'''
| align="center" style="background:#f0f0f0;"|'''Tube ID'''
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| NaiveESC.2||naïve ESCs cells||30.0
| NaiveESC.2||naïve ESCs cells||30.0
|}
|}
* ''' 10 MDS patients, known genotypes, (w/ Tiffany from Dr. Bejar's Lab)'''
=== G-MDS. 10 MDS patients, known genotypes, (w/ Tiffany from Dr. Bejar's Lab)===
* ''' K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Tiffany from Dr. Bejar's Lab)'''
=== G-K562. K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Tiffany from Dr. Bejar's Lab)===

Revision as of 17:15, 13 March 2015

Thesis Project Overview

Samples: Data analysis

  • Sample set codes starting with A.

A-Salk. Salk's Human Tissues Whole Genome Bisulfite Sequencing

  • Paper: Not out yet

A-BGI. Human peripheral mononuclear cells trio - type 2 diabetes - father, mother, daughter

A-WB. Human whole blood DNA methylation study - newborn, middle-age, centarian

Samples: Data generation

  • Sample set codes starting with G.

G-SS. Early definitive endoderm differentiation (Song's 3-days protocol and Sergio's H1 samples)

Tube ID Sample Concentration (QUBIT, ng/ul)
MA-16 H1 p54 Control TeSR 57.0
MA-17 H1 p54 Activin-A 40.1
AP-13 H1 p47 Control TeSR 85.0
AP-14 H1 p47 BMP-4 49.4
ESCd0.1 Day 0 ESCs 40.3
ESCd0.2 Day 0 ESCs 56.0
ESCd0.3 Day 0 ESCs 86.0
DE-d3.1 Day 3 definitive endoderm 34.0
DE-d3.2 Day 3 definitive endoderm 37.7
DE-d3.3 Day 3 definitive endoderm 25.7
NaiveESC.1 naïve ESCs cells 26.3
NaiveESC.2 naïve ESCs cells 30.0

G-MDS. 10 MDS patients, known genotypes, (w/ Tiffany from Dr. Bejar's Lab)

G-K562. K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Tiffany from Dr. Bejar's Lab)