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)=== | ||
{| class="wikitable" | |||
| align="center" style="background:#f0f0f0;"|'''Internal ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Sample_ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Number of mutated genes''' | |||
| align="center" style="background:#f0f0f0;"|'''Karyotype Group''' | |||
| align="center" style="background:#f0f0f0;"|'''U2AF1''' | |||
| align="center" style="background:#f0f0f0;"|'''DNMT3A''' | |||
| align="center" style="background:#f0f0f0;"|'''SF3B1''' | |||
| align="center" style="background:#f0f0f0;"|'''TET2''' | |||
| align="center" style="background:#f0f0f0;"|'''Primary Disease''' | |||
|- | |||
| MDS-T1||MDS_2006_32||1||-5q||||||||p.E852*||Myelodysplastic Syndrome | |||
|- | |||
| MDS-T2||MDS_2006_37||2||+8||p.S34F||p.R882H|||||| | |||
|- | |||
| MDS-T3||MDS_2006_52||2||-5q||||p.R736C||p.K700E||||Myelodysplastic Syndrome | |||
|- | |||
| MDS-T4||MDS_2006_90||0||+6|||||||||| | |||
|- | |||
| MDS-T5||MDS_2006_174||2||Normal||||||p.K700E||p.Q1537*|| | |||
|- | |||
| MDS-T6||MDS_2006_196||1||Normal||||||||p.K1339*||Myelodysplastic Syndrome | |||
|- | |||
| MDS-T7||MDS_2006_267||2||Normal||||p.R882C||p.K700E||||Myelodysplastic Syndrome | |||
|- | |||
| MDS-T8||MDS_2006_329||3||Normal||||p.W581R||p.K700E||p.Q531* p.D1402EfsX44||Myelodysplastic Syndrome | |||
|- | |||
| MDS-T9||UCSD control ||NA||NA||NA||NA||NA||NA||NA | |||
|- | |||
| MDS-T10||UCSD control ||NA||NA||NA||NA||NA||NA||NA | |||
|} | |||
=== 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)=== | ||
{| class="wikitable" | {| class="wikitable" |
Revision as of 21:55, 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)
Internal ID | Sample_ID | Number of mutated genes | Karyotype Group | U2AF1 | DNMT3A | SF3B1 | TET2 | Primary Disease |
MDS-T1 | MDS_2006_32 | 1 | -5q | p.E852* | Myelodysplastic Syndrome | |||
MDS-T2 | MDS_2006_37 | 2 | +8 | p.S34F | p.R882H | |||
MDS-T3 | MDS_2006_52 | 2 | -5q | p.R736C | p.K700E | Myelodysplastic Syndrome | ||
MDS-T4 | MDS_2006_90 | 0 | +6 | |||||
MDS-T5 | MDS_2006_174 | 2 | Normal | p.K700E | p.Q1537* | |||
MDS-T6 | MDS_2006_196 | 1 | Normal | p.K1339* | Myelodysplastic Syndrome | |||
MDS-T7 | MDS_2006_267 | 2 | Normal | p.R882C | p.K700E | Myelodysplastic Syndrome | ||
MDS-T8 | MDS_2006_329 | 3 | Normal | p.W581R | p.K700E | p.Q531* p.D1402EfsX44 | Myelodysplastic Syndrome | |
MDS-T9 | UCSD control | NA | NA | NA | NA | NA | NA | NA |
MDS-T10 | UCSD control | NA | NA | NA | NA | NA | NA | NA |
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 |