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)=== | ||
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| align="center" style="background:#f0f0f0;"|'''Sample ID''' | | align="center" style="background:#f0f0f0;"|'''Sample ID''' | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' |
Revision as of 21:42, 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 |