Dinh:Thesis Overview: Difference between revisions

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=Thesis Project Overview=
=Thesis Project Overview and Progress=
== Work flow charts ==
== Work flow charts ==
[[File:dna-methylation-analysis-workflow-dinh-031315.png | 600px]]
[[File:dna-methylation-workflow-dinh-031315.png | 1200px]]


==Samples: Data analysis (A) ==
==Programming works (P)==
* Sample set codes starting with A.
===P-BisReadMapper - Work on bisulfite reads mapper and analysis pipeline===
=== A-Salk. Salk's Human Tissues Whole Genome Bisulfite Sequencing ===
===P-LD.Block - Work on LD block finder===
===P-HapCluster - Work on Haplotype clustering===
==Data analysis (A) ==
=== Part 1 Progress: Data quality control ===
=== Part 2 Progress: Bisulfite reads mapping ===
=== Part 3 Progress: Processed bisulfite data storage and documentation ===
=== Part 4 Progress: High level analysis performed ===
===SAMPLES INFORMATION===
=== 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 ===
* Paper: http://www.ncbi.nlm.nih.gov/pubmed/23664764
 
=== A-Salk WGBS. Salk's Human Tissues Whole Genome Bisulfite Sequencing ===
* Paper: Not out yet
* Paper: Not out yet
=== A-BGI. Human peripheral mononuclear cells trio - type 2 diabetes - father, mother, daughter===
* Paper: http://genomebiology.com/2014/15/7/408
=== A-WB. Human whole blood DNA methylation study - newborn, middle-age, centarian===
* Paper: http://www.pnas.org/content/109/26/10522.full
==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)===
{| class="wikitable"
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Tube ID'''
| align="center" style="background:#f0f0f0;"|'''SampleName'''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Donor'''
| align="center" style="background:#f0f0f0;"|'''Concentration (QUBIT, ng/ul)'''
| align="center" style="background:#f0f0f0;"|'''Cell types'''
|-
| STL001BL-01 ||STL001 ||Bladder cells
|-
| STL001FT-01 ||STL001 ||Fat cells
|-
| STL001GA-01 ||STL001 ||Gastric cells
|-
| STL001LG-01 ||STL001 ||Lung cells
|-
|-
| MA-16||H1 p54 Control TeSR||57.0
| STL001LV-01 ||STL001 ||Left ventricle cells
|-
|-
| MA-17||H1 p54 Activin-A||40.1
| STL001PO-01 ||STL001 ||Psoas cells
|-
|-
| AP-13||H1 p47 Control TeSR||85.0
| STL001RV-01 ||STL001 ||Right ventricle cells
|-
|-
| AP-14||H1 p47 BMP-4||49.4
| STL001SB-01 ||STL001 ||Small bowel cells
|-
|-
| ESCd0.1||Day 0 ESCs||40.3
| STL001SG-01 ||STL001 ||Sigmoid colon cells
|-
|-
| ESCd0.2||Day 0 ESCs||56.0
| STL001SX-01 ||STL001 ||Spleen cells
|-
|-
| ESCd0.3||Day 0 ESCs||86.0
| STL001TH-01 ||STL001 ||Thymus tissue cells
|-
|-
| DE-d3.1||Day 3 definitive endoderm||34.0
| STL002AD-01 ||STL002 ||Adrenal cells
|-
|-
| DE-d3.2||Day 3 definitive endoderm||37.7
| STL002AO-01 ||STL002 ||Aorta cells
|-
|-
| DE-d3.3||Day 3 definitive endoderm||25.7
| STL002EG-01 ||STL002 ||Esophagus cells
|-
|-
| NaiveESC.1||naïve ESCs cells||26.3
| STL002FT-01 ||STL002 ||Fat cells
|-
|-
| NaiveESC.2||naïve ESCs cells||30.0
| STL002GA-01 ||STL002 ||Gastric cells
|}
=== 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
| STL002LG-01 ||STL002 ||Lung cells
|-
|-
| MDS-T2||MDS_2006_37||2||+8||p.S34F||p.R882H||||||
| STL002OV-01 ||STL002 ||Ovary tissue cells
|-
|-
| MDS-T3||MDS_2006_52||2||-5q||||p.R736C||p.K700E||||Myelodysplastic Syndrome
| STL002PA-01 ||STL002 ||Pancreas cells
|-
|-
| MDS-T4||MDS_2006_90||0||+6||||||||||
| STL002PO-01 ||STL002 ||Psoas cells
|-
|-
| MDS-T5||MDS_2006_174||2||Normal||||||p.K700E||p.Q1537*||
| STL002SB-01 ||STL002 ||Small bowel cells
|-
|-
| MDS-T6||MDS_2006_196||1||Normal||||||||p.K1339*||Myelodysplastic Syndrome
| STL002SX-01 ||STL002 ||Spleen cells
|-
|-
| MDS-T7||MDS_2006_267||2||Normal||||p.R882C||p.K700E||||Myelodysplastic Syndrome
| STL003AD-01 ||STL003 ||Adrenal cells
|-
|-
| MDS-T8||MDS_2006_329||3||Normal||||p.W581R||p.K700E||p.Q531* p.D1402EfsX44||Myelodysplastic Syndrome
| STL003AO-01 ||STL003 ||Aorta cells
|-
|-
| MDS-T9||UCSD control ||NA||NA||NA||NA||NA||NA||NA
| STL003EG-01 ||STL003 ||Esophagus cells
|-
|-
| MDS-T10||UCSD control ||NA||NA||NA||NA||NA||NA||NA
| STL003FT-01 ||STL003 ||Fat cells
|}
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Collaborator Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Concentration (ng/uL)'''
| align="center" style="background:#f0f0f0;"|'''Volume (uL)'''
| align="center" style="background:#f0f0f0;"|'''Volume BSPP (uL)'''
| align="center" style="background:#f0f0f0;"|'''Volume RRBS (uL)'''
| align="center" style="background:#f0f0f0;"|'''Remaning volume (uL)'''
| align="center" style="background:#f0f0f0;"|'''Remaining quantity DNA (ng)'''
| align="center" style="background:#f0f0f0;"|''''''
|-
|-
| MDS_2006_90||106.09||18.90||9.42||0.94||8.54||906.01||2005.03
| STL003GA-01 ||STL003 ||Gastric cells
|-
|-
| MDS_2006_174||93.12||21.50||10.74||1.07||9.69||902.33||2002.18
| STL003LV-01 ||STL003 ||Left ventricle cells
|-
|-
| MDS_2006_52||100.61||19.90||9.94||0.99||8.97||902.47||2002.13
| STL003PA-01 ||STL003 ||Pancreas cells
|-
|-
| MDS_2006_37||116.38||17.20||8.59||0.86||7.75||901.95||2001.75
| STL003PO-01 ||STL003 ||Psoas cells
|-
|-
| MDS_2006_329||112.44||17.80||8.89||0.89||8.02||901.77||2001.50
| STL003RA-01 ||STL003 ||Right atrium cells
|-
|-
| MDS_2006_32||103.69||19.30||9.64||0.96||8.70||902.10||2001.23
| STL003RV-01 ||STL003 ||Right ventricle cells
|-
|-
| MDS_2006_267||103.15||19.40||9.69||0.97||8.74||901.53||2001.11
| STL003SB-01 ||STL003 ||Small bowel cells
|-
|-
| MDS_2006_196||106.67||18.70||9.37||0.94||8.39||894.96||1994.72
| STL003SG-01 ||STL003 ||Sigmoid colon cells
|}
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''UCSD samples'''
| align="center" style="background:#f0f0f0;"|'''Concentration (ng/uL)'''
| align="center" style="background:#f0f0f0;"|'''Volume (uL)'''
| align="center" style="background:#f0f0f0;"|'''Volume BSPP (uL)'''
| align="center" style="background:#f0f0f0;"|'''Volume RRBS (uL)'''
| align="center" style="background:#f0f0f0;"|'''Remaining volume (uL)'''
| align="center" style="background:#f0f0f0;"|'''Remaining quantity DNA (ng)'''
|-
|-
| (MDS-T9) 40489562||31.7||200||31.55||3.15||165.3||5240
| STL003SX-01 ||STL003 ||Spleen cells
|-
|-
| (MDS-T10) 42397797||51.4||?||19.46||1.95||||
| STL011LI-01 ||STL011 ||Liver tissue cell
|}
|}


=== G-K562. K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Tiffany from Dr. Bejar's Lab)===
=== A-BGI. Human peripheral mononuclear cells trio - type 2 diabetes - father, mother, daughter===
* Paper: http://genomebiology.com/2014/15/7/408
=== A-WB. Human whole blood DNA methylation study - newborn, middle-age, centarian===
* Paper: http://www.pnas.org/content/109/26/10522.full
==Data generation (G) ==
===Part 1 Progress: Padlock probes capture with HOTSPOTS460K===
===Part 2 Progress: Design quality control DNA===
===Part 3 Progress: Perform quantification of 5hmC,5mC, and 5fC/5caC on samples===
=== SAMPLES INFORMATION ===
=== G-SS. Early definitive endoderm differentiation (Song's 3-days protocol and Sergio's H1 samples)===
{| class="wikitable"
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Tube ID'''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Info'''
| align="center" style="background:#f0f0f0;"|'''Concentration (QUBIT, ng/ul)'''
| align="center" style="background:#f0f0f0;"|'''Nanodrop (ng/uL)'''
|-
| align="center" style="background:#f0f0f0;"|'''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
|-
|-
| E10b ||Tet2, ||KO ||46.6 ||37.5
| ESCd0.3||Day 0 ESCs||86.0
|-
|-
| B10a ||Tet2, ||KO ||70.7 ||57
| DE-d3.1||Day 3 definitive endoderm||34.0
|-
|-
| C9 ||Tet2, ||WT ||55.2 ||39
| DE-d3.2||Day 3 definitive endoderm||37.7
|-
|-
| E4 ||Dnmt3a, ||KO ||60.4 ||52
| DE-d3.3||Day 3 definitive endoderm||25.7
|-
|-
| E10 ||Dnmt3a, ||KO ||47.3 ||41.8
| NaiveESC.1||naïve ESCs cells||26.3
|-
|-
| F1 ||Dnmt3a, ||WT ||55.7 ||41.2
| NaiveESC.2||naïve ESCs cells||30.0
|}
|}

Latest revision as of 18:15, 17 September 2015

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