Dinh:Thesis Overview: Difference between revisions

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=== G-MDS. 10 MDS patients, known genotypes, (w/ Tiffany from Dr. Bejar's Lab)===
=== 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
|-
| 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
|}
=== G-K562. K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Tiffany from Dr. Bejar's Lab)===
=== G-K562. K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Tiffany from Dr. Bejar's Lab)===
{| class="wikitable"
{| class="wikitable"

Revision as of 21:55, 17 March 2015

Thesis Project Overview

Work flow charts

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

Samples: Data analysis (A)

  • Sample set codes starting with A.

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

  • Paper: Not out yet

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

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