Dinh:Thesis Overview: Difference between revisions
Jump to navigation
Jump to search
>Dinh |
>Dinh mNo edit summary |
||
(7 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
=Thesis Project Overview= | =Thesis Project Overview and Progress= | ||
== Work flow charts == | == Work flow charts == | ||
[[File:dna-methylation-workflow-dinh-031315.png | 1200px]] | [[File:dna-methylation-workflow-dinh-031315.png | 1200px]] | ||
== | ==Programming works (P)== | ||
* | ===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 | ||
{| class="wikitable" | {| class="wikitable" | ||
| align="center" style="background:#f0f0f0;"|''' | | align="center" style="background:#f0f0f0;"|'''SampleName''' | ||
| align="center" style="background:#f0f0f0;"|''' | | align="center" style="background:#f0f0f0;"|'''Donor''' | ||
| align="center" style="background:#f0f0f0;"|''' | | 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 | |||
|- | |- | ||
| | | 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=== | ||
* 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;"|''' | | align="center" style="background:#f0f0f0;"|'''Tube ID''' | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' | ||
| align="center" style="background:#f0f0f0;"|''' | | align="center" style="background:#f0f0f0;"|'''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 | ||
|} | |} |
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 |