Dinh:Thesis Overview: Difference between revisions

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>Dinh
>Dinh
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|-
|-
| MDS-T10||UCSD control ||NA||NA||NA||NA||NA||NA||NA
| MDS-T10||UCSD control ||NA||NA||NA||NA||NA||NA||NA
|}
{| 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
|-
| 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
|}
|}



Revision as of 21:57, 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
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

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