Dinh:Thesis Overview: Difference between revisions

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=== G-MDS. 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)===
=== G-K562. 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)===
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Info'''
| align="center" style="background:#f0f0f0;"|'''Nanodrop (ng/uL)'''
| align="center" style="background:#f0f0f0;"|'''Qubit (ng/uL)'''
|-
| E10b ||Tet2, ||KO ||46.6 ||37.5
|-
| B10a ||Tet2, ||KO ||70.7 ||57
|-
| C9 ||Tet2, ||WT ||55.2 ||39
|-
| E4 ||Dnmt3a, ||KO ||60.4 ||52
|-
| E10 ||Dnmt3a, ||KO ||47.3 ||41.8
|-
| F1 ||Dnmt3a, ||WT ||55.7 ||41.2
|}

Revision as of 21:41, 17 March 2015

Thesis Project Overview

Work flow charts

File:Dna-methylation-analysis-workflow-dinh-031315.png

Samples: Data analysis (A)

  • 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 (G)

  • 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)

Sample ID Sample Info Nanodrop (ng/uL) Qubit (ng/uL)
E10b Tet2, KO 46.6 37.5
B10a Tet2, KO 70.7 57
C9 Tet2, WT 55.2 39
E4 Dnmt3a, KO 60.4 52
E10 Dnmt3a, KO 47.3 41.8
F1 Dnmt3a, WT 55.7 41.2