Thesis Project Overview and Progress[edit]
Work flow charts[edit]
File:Dna-methylation-workflow-dinh-031315.png
Programming works (P)[edit]
P-BisReadMapper - Work on bisulfite reads mapper and analysis pipeline[edit]
P-LD.Block - Work on LD block finder[edit]
P-HapCluster - Work on Haplotype clustering[edit]
Data analysis (A)[edit]
Part 1 Progress: Data quality control[edit]
Part 2 Progress: Bisulfite reads mapping[edit]
Part 3 Progress: Processed bisulfite data storage and documentation[edit]
Part 4 Progress: High level analysis performed[edit]
SAMPLES INFORMATION[edit]
A-N37 WGBS. Low coverage whole genome BS generated by our lab[edit]
A-Development WGBS. Bing Ren's lab early embryonic development from H1 ESCs[edit]
A-Salk WGBS. Salk's Human Tissues Whole Genome Bisulfite Sequencing[edit]
SampleName
|
Donor
|
Cell types
|
STL001BL-01 |
STL001 |
Bladder cells
|
STL001FT-01 |
STL001 |
Fat cells
|
STL001GA-01 |
STL001 |
Gastric cells
|
STL001LG-01 |
STL001 |
Lung cells
|
STL001LV-01 |
STL001 |
Left ventricle cells
|
STL001PO-01 |
STL001 |
Psoas cells
|
STL001RV-01 |
STL001 |
Right ventricle cells
|
STL001SB-01 |
STL001 |
Small bowel cells
|
STL001SG-01 |
STL001 |
Sigmoid colon cells
|
STL001SX-01 |
STL001 |
Spleen cells
|
STL001TH-01 |
STL001 |
Thymus tissue cells
|
STL002AD-01 |
STL002 |
Adrenal cells
|
STL002AO-01 |
STL002 |
Aorta cells
|
STL002EG-01 |
STL002 |
Esophagus cells
|
STL002FT-01 |
STL002 |
Fat cells
|
STL002GA-01 |
STL002 |
Gastric cells
|
STL002LG-01 |
STL002 |
Lung cells
|
STL002OV-01 |
STL002 |
Ovary tissue cells
|
STL002PA-01 |
STL002 |
Pancreas cells
|
STL002PO-01 |
STL002 |
Psoas cells
|
STL002SB-01 |
STL002 |
Small bowel cells
|
STL002SX-01 |
STL002 |
Spleen cells
|
STL003AD-01 |
STL003 |
Adrenal cells
|
STL003AO-01 |
STL003 |
Aorta cells
|
STL003EG-01 |
STL003 |
Esophagus cells
|
STL003FT-01 |
STL003 |
Fat cells
|
STL003GA-01 |
STL003 |
Gastric cells
|
STL003LV-01 |
STL003 |
Left ventricle cells
|
STL003PA-01 |
STL003 |
Pancreas cells
|
STL003PO-01 |
STL003 |
Psoas cells
|
STL003RA-01 |
STL003 |
Right atrium cells
|
STL003RV-01 |
STL003 |
Right ventricle cells
|
STL003SB-01 |
STL003 |
Small bowel cells
|
STL003SG-01 |
STL003 |
Sigmoid colon cells
|
STL003SX-01 |
STL003 |
Spleen cells
|
STL011LI-01 |
STL011 |
Liver tissue cell
|
A-BGI. Human peripheral mononuclear cells trio - type 2 diabetes - father, mother, daughter[edit]
A-WB. Human whole blood DNA methylation study - newborn, middle-age, centarian[edit]
Data generation (G)[edit]
Part 1 Progress: Padlock probes capture with HOTSPOTS460K[edit]
Part 2 Progress: Design quality control DNA[edit]
Part 3 Progress: Perform quantification of 5hmC,5mC, and 5fC/5caC on samples[edit]
SAMPLES INFORMATION[edit]
G-SS. Early definitive endoderm differentiation (Song's 3-days protocol and Sergio's H1 samples)[edit]
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
|