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= May 19, 2011, gDNA from the blood samples of HIV patients, UCSD Medical School =
= May 19, 2011, gDNA from the blood samples of HIV patients, UCSD Medical School =
* Received 39 samples from sué Pérez-Santiago (from Christopher Woelk's lab, UCSD medical School)
* Received 39 samples from Josué Pérez-Santiago (from Christopher Woelk's lab, UCSD medical School)
* Each sample volume 21ul, conc. 100ng/ul
* Each sample volume 21ul, conc. 100ng/ul
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{| {{table}} border = 1

Revision as of 14:44, 28 May 2011

November5, 2010 (Mouse gDNA from La Spada's lab, UCSD)

  • received 8 gDNA samples from Paula Ladd
Samples Sample ID concentration (ng/ul) volume (ul)
1. wild-type cortex WT-CTX 2000.0 3.8
2. wild-type cerebellum WT-CBL 100.0 8.2
3. wild-type brain stem WT-BS 600.0 8.5
4. wild-type retina WT-RET 1800.0 4.0
5. transgenic cortex TG-CTX 250.0 17.0
6. transgenic cerebellum TG-CBL 400.0 14.0
7. transgenic brain stem TG-BS 1000.0 6.5
8. transgenic retina TG-RET 2000.0 8.0
Note: WT: wild-type, TG: transgenic
Samples were diluted to 200ng/ul based on original concentration from Paula and confirmed by Nanodrop
Samples Sample ID total volume (ul) after diluted concentration(ng/ul)
1. wild-type cortex WT-CTX 25.0 223.2
2. wild-type cerebellum WT-CBL 25.0 663.5
3. wild-type brain stem WT-BS 25.0 86.0
4. wild-type retina WT-RET 25.0 163.7
5. transgenic cortex TG-CTX 20.0 219.2
6. transgenic cerebellum TG-CBL 25.0 109.4
7. transgenic brain stem TG-BS 25.0 103.0
8. transgenic retina TG-RET 25.0 126.6


labnote: 2010_11_08


December 7, 2010 (Sarah's African gDNA, UPenn )

  • received 48 methylome samples from Tishkoff's lab delivered by UPS

William R Beggs, Jr.
Tishkoff Lab - Dept of Genetics, University of Pennsylvania
430 Clinical Research Building
415 Curie Blvd
Philadelphia, PA 19104-6145

LabID 1M sample # Well Volume ul Conc ng/ul approx
CAPB016 A01 50 100
CAPB046 B01 50 100
CAPB056a C01 50 100
CAPL056 D01 50 100
CAPM007 E01 50 100
TZHZ018A F01 50 100
TZHZ033B G01 50 100
TZHZ075A H01 50 100
TZHZ214 A02 50 100
TZHZ221B B02 50 100
TZSW067 C02 50 100
TZSW128B D02 50 100
TZSW131A E02 50 100
TZSW132B F02 50 100
TZSW135B G02 50 100
CAMF013A H02 50 100
CAFU043 A03 50 100
CAFU042 B03 50 100
CAFU028 C03 50 100
CAMF022A D03 50 100
CAPB043 E03 50 100
CAPL049 F03 50 100
CAPM001A G03 50 100
CAPL036 H03 50 100
KEBR007A A04 50 100
KEBR028A B04 50 100
KEBR042B C04 50 100
KEBR040A D04 50 100
KEBR061A E04 50 100
KEPK003A F04 50 100
KEPK006A G04 50 100
KEPK007A H04 50 100
KEPK010A A05 50 100
KEPK016A B05 50 100
CAPM047 son C05 50 100
CAPM003A parent D05 50 100
CAPM004A parent E05 50 100
CAPM056A daughter F05 50 100
ETAM042 G05 50 100
ETAM071 H05 50 100
ETAM077 A06 50 100
ETAM058 B06 50 100
ETAM065 C06 50 100
ETSB008 D06 50 100
ETSB027 E06 50 100
ETSB031 F06 50 100
ETSB035 G06 50 100
ETSB036 H06 50 100

December 10, 2010 (normal/tumor gDNA from JHU)

  • received 48 normal/tumor gDNA samples from JHU delivered by FedEx

Eirikur Briem
John Hopkins University
855N. Wolfe Street
Rangos 580.14
Baltimore, MD 21205

Sample_ID Kun_Well Final Volume (uL) Final_Conc (ng/uL)
395 G3 50 30
970 H4 50 30
12 A1 50 30
258 F2 50 30
299 A3 50 30
335 C3 50 30
440 A5 50 30
503 E5 50 30
736 G6 50 30
895 F4 50 30
84 E1 50 30
198 H1 50 30
203 B2 50 30
368 E3 50 30
388 F3 50 30
436 H3 50 30
524 F5 50 30
686 F6 50 30
48 C1 50 30
85 F1 50 30
107 G1 50 30
253 D2 50 30
467 D5 50 30
569 H5 50 30
850 B4 50 30
894 E4 50 30
893 D4 30 50
659 E6 30 50
538 G5 30 50
967 G4 30 50
304 B3 30 50
256 E2 30 50
42 B1 30 50
77 D1 30 50
201 A2 30 50
222 C2 30 50
280 G2 30 50
282 H2 30 50
362 D3 30 50
445 B5 30 50
455 C5 30 50
572 A6 30 50
607 B6 30 50
619 C6 30 50
621 D6 30 50
743 H6 30 50
791 A4 30 50
881 C4 30 50
  • sort out sample ID into plate layout
Plate layout 1 2 3 4 5 6
A 12 201 299 791 440 572
B 42 203 304 850 445 607
C 48 222 335 881 455 619
D 77 253 362 893 467 621
E 84 256 368 894 503 659
F 85 258 388 895 524 686
G 107 280 395 967 538 736
H 198 282 436 970 569 743

December 16, 2010 (Bisulfite converted mouse gDNA from JHU)

  • received 4 bisulfite converted mouse gDNA from Yuan Gao

Yuan Gao
Forrest City Baltimore
855 N. Wolfe St. STE 102
Baltimore, MD 21205

Sample ID Conc. (ng/ul) confirmed by Qubit Volume (ul) Total amount (ng)
WT 2.40 7.00 16.80
WT ECT 5.54 6.00 33.24
G45B KO 3.04 7.00 21.28
G45B ECT KO 4.14 6.00 24.84


February 2, 2011 (Brain gDNA of Parkinson's patients from Burnham Institute, human frozen cerebral cortex)

  • Received 18 human brain samples from Parkinson's patients. This includes control and Parkinson's patient samples.
Pair Control Sample ID Sample code Sex age (year.day) Postmortem time Conc. (ug/ul)/ volume (ul) PD Sample ID Sample code Sex age (year.day) Postmortem time Conc. (ug/ul)/ volume (ul)
1 5028 P1C M 67.293 P18 0.5ug/ul/ 4ul 1947 P1P M 70.251 P17 0.5ug/ul/ 4ul
2 4789 P2C F 72.053 P19 0.5ug/ul/ 4ul 4977 P2P F 76.081 P14 0.5ug/ul/ 4ul
3 5171 P3C M 79.088 P05 0.5ug/ul/ 4ul 4879 P3P M 75.351 P15 0.5ug/ul/ 4ul
4 1818 P4C M 76.294 P03 0.5ug/ul/ 4ul 4526 P4P M 78.182 P01 0.5ug/ul/ 4ul
5 5089 P5C M 89.018 P14 0.5ug/ul/ 4ul 5203 P5P M 89.06 P10 0.5ug/ul/ 4ul
6 5237 P6C M 52.291 P13 0.5ug/ul/ 4ul 1910 P6P M 51.243 P10 0.5ug/ul/ 4ul
7 1569 P7C1 F 77.089 P08 0.5ug/ul/ 4ul 1401 P7P F 80.215 P04 0.5ug/ul/ 4ul
7 5219 P7C2 F 76.348 P03 0.5ug/ul/ 4ul
8 4735 P8C M 73.184 P21 0.5ug/ul/ 4ul 1741 P8P1 M 71.348 P20 0.5ug/ul/ 4ul
8 5306 P8P2 M 76.311 P21 0.5ug/ul/ 4ul


  • related lab note:
  • Data analysis:

March 10, 2011, Cell pellet samples from Belmonte's lab, Salk Institute

  • Received 5 cell pellet samples from Belmonte's lab
  • Extracted gDNA using DNeasy Blood and Tissue kit (Qiagen)
Samples No. of cell gDNA conc. (ng/ul) Elution volume (ul) Yields (ug)
1. HGPS 1.0E6 75.7 300 22.71
2. cHGPS1 1.0E6 57.1 300 17.13
3. cHGPS40 1.0E6 100.2 300 30.06
4. AWS 1.0E6 42.2 300 12.66
5. cAWS1 1.0E6 130.1 300 39.03
  • related lab note:
  • Data analysis:

April 21, 2011, PGP1 iPS gDNA from Harvard

  • Received one sample of PGP1 CD1 iPS P16 from Harvard Medical School

Jihyuk Lee
Harvard Medical School
77 Avenue Louis Pasteur
Boston, MA 02115

Sample name Sample ID Conc. (ng/ul) Total amount (ug)
PGP1 CD1 iPS P16 PGP1 iPS 129 39


April 27, 2011, gDNA of TET study from Harvard Medical School

  • Received 24 gDNA sample from Yeguang (from Yujiang Geno Shi's lab)
Tube Number Sample description concentration (ng/ul) 9 sample choice 12 sample choice
#1 Scr-1 117.1 X X
#2 Sh3513-1 116.5 X X
#3 Sh1-1 80.3 X
#4 Scr-2 235 X
#5 Sh3513-2 313 X
#6 Sh1-2 142 X
#7 Mock 117 X X
#8 TET2-35# 113 X X
#9 TET2-75# 138 X X
#10 HMEC-Scr 215 X X
#11 HMEC-Sh3513 246 X X
#12 HMEC-Sh1 51.3 X
#13 Scr-3 161 X
#14 Sh3513-3 159 X
#15 T2-SCr-1 186
#16 T2m-Scr-1 187
#17 T2-Scr-2 298
#18 T2m-Scr-2 291
#19 NB4-Scr 93.9
#20 NB4-Sh3513 53.8
#21 NB4-Sh2513 74.6
#22 NB4-Sh5372 77.8
#23 NB4-T2 89.5
#24 NB4-T2m 138.4


  • Related lab note: [[10]]

May 19, 2011, gDNA from the blood samples of HIV patients, UCSD Medical School

  • Received 39 samples from Josué Pérez-Santiago (from Christopher Woelk's lab, UCSD medical School)
  • Each sample volume 21ul, conc. 100ng/ul
Sample ID PID Place in 96plate Volume (ul) Conc. (ng/ul) Total amount (ug)
3 26406 102 A1 21 100 2.1
4 26406 108 A2 21 100 2.1
5 26604 054 A3 21 100 2.1
6 26604 066 A4 21 100 2.1
11 NW578 000 A5 21 100 2.1
12 NW578 012 A6 21 100 2.1
13 58346 006 A7 21 100 2.1
14 58346 012 A8 21 100 2.1
15 CA198 006 A9 21 100 2.1
16 CA198 C12 A10 21 100 2.1
17 CA219 000 A11 21 100 2.1
18 CA219 006 A12 21 100 2.1
19 CA275 000 B1 21 100 2.1
20 CA275 006 B2 21 100 2.1
21 CB252 000 B3 21 100 2.1
22 CB252 006 B4 21 100 2.1
24 CC182 012 B5 21 100 2.1
25 24371 000 B6 21 100 2.1
26 24371 012 B7 21 100 2.1
27 NW470 012 B8 21 100 2.1
28 NW470 024 B9 21 100 2.1
30 27054 012 B10 21 100 2.1
31 CA239 000 B11 21 100 2.1
33 CE214 000 B12 21 100 2.1
34 CE214 006 C1 21 100 2.1
35 CB255 000 C2 21 100 2.1
36 CB255 006 C3 21 100 2.1
37 21003 000 C4 21 100 2.1
38 21003 012 C5 21 100 2.1
39 CG139 006 C6 21 100 2.1
40 CG139 018 C7 21 100 2.1
41 NM633 012 C8 21 100 2.1
42 NM633 024 C9 21 100 2.1
43 NM805 012 C10 21 100 2.1
44 NM805 024 C11 21 100 2.1
45 CB199 000 C12 21 100 2.1
46 26592 060 D1 21 100 2.1
47 24054 030 D2 21 100 2.1
48 24054 036 D3 21 100 2.1


May 25, 2011, gDNA from Jin Standforf Univ

  • Received gDNA samples for all the tissues of individual N37 from Jin Billi Li, Standford Univ.

Jin Billy Li
Standford University Genetics Dept.
Standford Univ ALWAY BLDG M-341
259 CAMPUS DR ALWAY BLDG Standford, CA 94035

Number Sample Concentration (ug/ul) Volume (ul) Total amount (ug) NewID
1.00 Cerebellum 1.38 1.45 2.00 N37-1
2.00 Colon 1.44 1.39 2.00 N37-2
3.00 Frontal lobe 0.91 2.20 2.00 N37-3
4.00 Heart 0.73 2.74 2.00 N37-4
5.00 Small intestine 1.09 1.83 1.99 N37-5
6.00 Liver 0.93 2.15 2.00 N37-6
7.00 Lung 0.50 4.00 2.00 N37-7
8.00 Skeletal muscle 0.57 3.51 2.00 N37-8
9.00 Pancrease 1.48 1.35 2.00 N37-9
10.00 Stomach 1.17 1.71 2.00 N37-10