Revision as of 21:55, 17 March 2015 by >Dinh
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
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
|