Dinh:Thesis Overview
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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]
- Paper: Not out yet
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 |