Dinh:Thesis Overview

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Thesis Project Overview

Work flow charts

File:Dna-methylation-workflow-dinh-031315.png

Programming works (P)

P-BisReadMapper - Work on bisulfite reads mapper and analysis pipeline

P-LD.Block - Work on LD block finder

P-HapCluster - Work on Haplotype clustering

Samples: Data analysis (A)

A-N37 WGBS. Low coverage whole genome BS generated by our lab

A-Development WGBS. Bing Ren's lab early embryonic development from H1 ESCs

A-Salk WGBS. Salk's Human Tissues Whole Genome Bisulfite Sequencing

  • 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

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
Collaborator Sample ID Concentration (ng/uL) Volume (uL) Volume BSPP (uL) Volume RRBS (uL) Remaning volume (uL) Remaining quantity DNA (ng) '
MDS_2006_90 106.09 18.90 9.42 0.94 8.54 906.01 2005.03
MDS_2006_174 93.12 21.50 10.74 1.07 9.69 902.33 2002.18
MDS_2006_52 100.61 19.90 9.94 0.99 8.97 902.47 2002.13
MDS_2006_37 116.38 17.20 8.59 0.86 7.75 901.95 2001.75
MDS_2006_329 112.44 17.80 8.89 0.89 8.02 901.77 2001.50
MDS_2006_32 103.69 19.30 9.64 0.96 8.70 902.10 2001.23
MDS_2006_267 103.15 19.40 9.69 0.97 8.74 901.53 2001.11
MDS_2006_196 106.67 18.70 9.37 0.94 8.39 894.96 1994.72
UCSD samples Concentration (ng/uL) Volume (uL) Volume BSPP (uL) Volume RRBS (uL) Remaining volume (uL) Remaining quantity DNA (ng)
(MDS-T9) 40489562 31.7 200 31.55 3.15 165.3 5240
(MDS-T10) 42397797 51.4 ? 19.46 1.95

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