Dinh:Thesis Overview: Difference between revisions
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| MDS-T8||MDS_2006_329||3||Normal||||p.W581R||p.K700E||p.Q531* p.D1402EfsX44||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|| | | MDS-T9||UCSD control ||NA||NA||NA||NA||NA||NA||Myelodysplastic Syndrome | ||
|- | |- | ||
| MDS-T10||UCSD control ||NA||NA||NA||NA||NA||NA|| | | MDS-T10||UCSD control ||NA||NA||NA||NA||NA||NA||Myelodysplastic Syndrome | ||
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{| class="wikitable" | {| class="wikitable" |
Revision as of 16:47, 22 April 2015
Thesis Project Overview and Progress
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
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
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
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)
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 | Myelodysplastic Syndrome |
MDS-T10 | UCSD control | NA | NA | NA | NA | NA | NA | Myelodysplastic Syndrome |
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 |