Dinh:Projects/MDS

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10 MDS patients, known genotypes, (w/ Tiffany from Dr. Bejar's Lab)[edit]

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

K562. K562 cell lines: TET2 knockout (2), DNMT3a knockout (2), wildtype (2), (w/ Brian Reilly from Dr. Bejar's Lab)[edit]

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