Noi:Sample tracking

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2014 sample tracking[edit]

March 18, 2014 (BSC samples from Illumina)[edit]

BSC samples from Illumina[edit]

- Received 12 BSC sample derived from amplified and un-amplified circulating tumor DNA from patients from Illumina

Sample_ID Sample_wel BSC input (ng) Preamp? Conc. (ng/ul) Volume (ul)
BSC_10ng_restored_1-1 A1 10 Yes 569.3 10
BSC_10ng_restored_1-2 A2 10 Yes 577.6 10
BSC_1ng_restored_1-1 A3 1 Yes 427.9 10
BSC_1ng_restored_1-2 A4 1 Yes 437.0 10
BSC_10ng_restored_2-1 A5 10 Yes 546.8 10
BSC_10ng_restored_2-2 A6 10 Yes 494.3 10
BSC_1ng_restored_2-1 A7 1 Yes 338.8 10
BSC_1ng_restored_2-2 A8 1 Yes 358.0 10
BSC_80ng_restored A9 80 Yes 566.7 10
BSC_30ng_restored A10 30 Yes 615.3 10
BSC_80ng B1 80 No 8.0 10
BSC_30ng_1 B2 30 No 3.0 10
BSC_30ng_2 B3 30 No 3.0 10
  • The concentration of these samples were changed because I added more TE buffer and re-quantified concentration by Qubit quantification

April 14, 2014 (8 additional amplified DNA samples from Illumina)[edit]

  • Received 8 additional amplified DNA samples from Xuyu Cai
  • No information of sample was provide only 5ul for each one and concentration ~200ng/ul
  • I added more H2O to bring volume to 12ul, transfered samples to 8-tube strip with individual cap, and re-quantified concentration with Qubit ssDNA HS assay

Qubit dsDNA assay HS results[edit]

Sample Conc. in the Qubit Unit uL used Dilution Sample conc. (ng/ul) Total volume Total amount (ng)
#1 173 ng/mL 1 200 34.6 12 415.2
#2 152 ng/mL 1 200 30.4 12 364.8
#3 199 ng/mL 1 200 39.9 12 478.8
#4 207 ng/mL 1 200 41.4 12 496.8
#5 108 ng/mL 1 200 21.6 12 259.2
#6 154 ng/mL 1 200 30.9 12 370.8
#7 181 ng/mL 1 200 36.1 12 433.2
#8 172 ng/mL 1 200 34.4 12 412.8

5-06-2014

  • Received ~30ul of polymerase with property similar to Amplitaq Stoffel fragment. Conc. 3U/ul. She is not allowed to provide any further info. of this enzyme.

May 22, 2014 (Plasma samples from normal samples with no cancer history[edit]

  • Received 30 plasma samples 1mL each from Kang Zhang's lab
  • All samples were collected in 2014
Zhang Id phenotype_category sex date_of_birth Age ethnicity
15849001 Normal - Other M 2/13/1946 68 Caucasian - European
15898001 Normal Control F 1/21/1983 31 Caucasian - European
16188001 Normal Control M 2/21/1954 60 Caucasian - European
16191001 Normal Control M 9/25/1964 50 Caucasian - European
16296003 Normal Control F 8/8/1976 38 Caucasian - European
16345002 Normal Control F 3/31/1986 28 Caucasian - European
16405003 Normal Control F 8/9/1960 54 Caucasian - European
16408001 Normal Control M 3/12/1944 70 Caucasian - European
16409002 Normal Control F 10/30/1943 71 Caucasian - European
16409003 Normal Control M 8/10/1971 43 Caucasian - European
16416001 Normal Control F 11/4/1949 65 Caucasian - European
16461001 Normal Control F 1/31/1936 78 Caucasian - European
16508001 Normal Control M 8/13/1973 41 Caucasian - European
16509001 Normal Control F 3/8/1964 50 Caucasian - European
16510002 Normal Control M 8/26/1957 57 Caucasian - European
16512001 Normal Control M 6/1/1982 32 Caucasian - European
16517001 Normal Control M 4/3/1949 65 Caucasian - European
16518001 Normal Control M 1/18/1955 59 Caucasian - European
16519001 Normal Control F 6/13/1976 38 Caucasian - European
16520001 Normal Control M 12/30/1954 60 Caucasian - European
16523001 Normal Control M 7/8/1955 59 Caucasian - European
16524001 Normal Control F 1/11/1953 61 Caucasian - European
16534001 Normal Control F 3/4/1992 22 Caucasian - European
16553001 Normal Control F 3/11/1938 76 Caucasian - European
16557001 Normal Control M 6/8/1948 66 Caucasian - European
16561001 Normal Control F 8/28/1972 42 Caucasian - European
16562001 Normal Control M 3/8/1983 31 Caucasian - European
16563001 Normal Control M 1/31/1954 60 Caucasian - European
16564001 Normal Control F 2/23/1986 28 Caucasian - European
16565001 Normal Control F 10/22/1968 46 Caucasian - European

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

  • 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 )[edit]

  • 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)[edit]

  • 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)[edit]

  • 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)[edit]

  • 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[edit]

  • 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[edit]

  • 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


  • Related lab note:
  • Mapping data:

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

  • 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:
  • Mapping data:

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

  • 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 of 10 different tissues from Billi Li, Standforf Univ[edit]

  • 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


  • Related lab note:
  • Mapping data:

July 8, 2011, gDNA from the blood samples of control and GA patients from Kang Zhang's lab, UCSD[edit]

  • Received 48 control and 48 GA gDNA blood samples (GA methylation plate1) from Zhao Ling (Dr. Kang Zhang's post doc)
  • The concentration of every samples was adjusted to 100ng/ul, total amount 2ug.

Sample number Well Phenotype ID
GA-methylation plate1-1 A1 GA 565003
GA-methylation plate1-2 B1 GA 773002
GA-methylation plate1-3 C1 GA 786015
GA-methylation plate1-4 D1 GA 788001
GA-methylation plate1-5 E1 GA 819002
GA-methylation plate1-6 F1 GA 875012
GA-methylation plate1-7 G1 GA 881006
GA-methylation plate1-8 H1 GA 1069001
GA-methylation plate1-9 A2 GA 1100001
GA-methylation plate1-10 B2 GA 1104001
GA-methylation plate1-11 C2 GA 1150004
GA-methylation plate1-12 D2 GA 1191002
GA-methylation plate1-13 E2 GA 1271001
GA-methylation plate1-14 F2 GA 1315001
GA-methylation plate1-15 G2 GA 1378001
GA-methylation plate1-16 H2 GA 1447001
GA-methylation plate1-17 A3 GA 1592002
GA-methylation plate1-18 B3 GA 1603001
GA-methylation plate1-19 C3 GA 1977001
GA-methylation plate1-20 D3 GA 2030010
GA-methylation plate1-21 E3 GA 2200001
GA-methylation plate1-22 F3 GA 2274002
GA-methylation plate1-23 G3 GA 2456001
GA-methylation plate1-24 H3 GA 2939001
GA-methylation plate1-25 A4 GA 2996001
GA-methylation plate1-26 B4 GA 4705001
GA-methylation plate1-27 C4 GA 5462001
GA-methylation plate1-28 D4 GA 6001001
GA-methylation plate1-29 E4 GA 6035002
GA-methylation plate1-30 F4 GA 6328001
GA-methylation plate1-31 G4 GA 10004001
GA-methylation plate1-32 H4 GA 11402001
GA-methylation plate1-33 A5 GA 11596001
GA-methylation plate1-34 B5 GA 11597001
GA-methylation plate1-35 C5 GA 11599001
GA-methylation plate1-36 D5 GA 11622001
GA-methylation plate1-37 E5 GA 11923001
GA-methylation plate1-38 F5 GA 12113001
GA-methylation plate1-39 G5 GA 12556001
GA-methylation plate1-40 H5 GA 12622001
GA-methylation plate1-41 A6 GA 12625001
GA-methylation plate1-42 B6 GA 12687001
GA-methylation plate1-43 C6 GA 12967001
GA-methylation plate1-44 D6 GA 13174001
GA-methylation plate1-45 E6 GA 13447001
GA-methylation plate1-46 F6 GA 13976001
GA-methylation plate1-47 G6 GA 14033001
GA-methylation plate1-48 H6 GA 14137001
GA-methylation plate1-49 A7 Control 825002
GA-methylation plate1-50 B7 Control 880003
GA-methylation plate1-51 C7 Control 888003
GA-methylation plate1-52 D7 Control 1373001
GA-methylation plate1-53 E7 Control 6925001
GA-methylation plate1-54 F7 Control 6988001
GA-methylation plate1-55 G7 Control 7161001
GA-methylation plate1-56 H7 Control 7419001
GA-methylation plate1-57 A8 Control 7528001
GA-methylation plate1-58 B8 Control 7529001
GA-methylation plate1-59 C8 Control 7729002
GA-methylation plate1-60 D8 Control 7781002
GA-methylation plate1-61 E8 Control 10174001
GA-methylation plate1-62 F8 Control 10182001
GA-methylation plate1-63 G8 Control 10214001
GA-methylation plate1-64 H8 Control 10223001
GA-methylation plate1-65 A9 Control 10272001
GA-methylation plate1-66 B9 Control 10555001
GA-methylation plate1-67 C9 Control 10703001
GA-methylation plate1-68 D9 Control 10741001
GA-methylation plate1-69 E9 Control 10914001
GA-methylation plate1-70 F9 Control 10958001
GA-methylation plate1-71 G9 Control 11029001
GA-methylation plate1-72 H9 Control 11066001
GA-methylation plate1-73 A10 Control 11167001
GA-methylation plate1-74 B10 Control 11198001
GA-methylation plate1-75 C10 Control 11200001
GA-methylation plate1-76 D10 Control 11201001
GA-methylation plate1-77 E10 Control 11202001
GA-methylation plate1-78 F10 Control 11210001
GA-methylation plate1-79 G10 Control 11285001
GA-methylation plate1-80 H10 Control 11324001
GA-methylation plate1-81 A11 Control 11340001
GA-methylation plate1-82 B11 Control 11379001
GA-methylation plate1-83 C11 Control 11394002
GA-methylation plate1-84 D11 Control 11424001
GA-methylation plate1-85 E11 Control 11434001
GA-methylation plate1-86 F11 Control 11585001
GA-methylation plate1-87 G11 Control 11594001
GA-methylation plate1-88 H11 Control 11595001
GA-methylation plate1-89 A12 Control 11720001
GA-methylation plate1-90 B12 Control 11748001
GA-methylation plate1-91 C12 Control 11756001
GA-methylation plate1-92 D12 Control 11779001
GA-methylation plate1-93 E12 Control 11783001
GA-methylation plate1-94 F12 Control 11790001
GA-methylation plate1-95 G12 Control 11792001
GA-methylation plate1-96 H12 Control 11793001


  • GA-methylation plate1: Media:GA_methylation_sample_plate1.xlsx
  • Note: Since the capture of the GA plate1 failed, and I needed to repeated the experiment, Ling brought the new plate (called GA plate1-2) with the same samples to me and all concentration were measured again by Nanodrop.
  • Related lab note:
    • [[18]] (the experiment which the capture failed)
    • [[19]]

July 29, 2011, gDNA of 3 human iPS lines with single nonsynonymous mutations, UCSD[edit]

  • Received 3 gDNA sample from Alice that are iPS lines with single nonsynonymous mutation)
    • 1) 2HFF 8d_10, conc. by Nanodrop: 214.60 ng/ul
    • 2) 218HHF211, conc. by Nanodrop: 411.10 ng/ul
    • 3) 218HHF411, conc. by Nanodrop: 359.60 ng/ul
  • Related lab note:

August 1, 2011, gDNA of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA[edit]

  • Received 96 gDNA samples (in 96-well plate) of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA

Eric Strengman
UCLA 695 Charles E. Young Dr. S
Gonda 4335
Los Angeles, CA 90095

  • Each sample was remeasured the DNA conc. by Nanodrop
  • Related lab note:
  • Note: Since I thought that they all are brain tissue samples, some labeling of library name or images used brain instead of blood. To prevent confusing, every labeling should be changed.

August25, 2011, gDNA from fibroblast cells that are the somatic line of the three single nonsynonymous mutation iPS on the record of July29, 2011[edit]

  • Received 2 gDNA samples from fibroblast cells that are the somatic lines of the three single nonsynonymous mutation iPS from Alice. Both of them were from the first elution in DNA purification
Sample ID Conc. (ng/ul) by Sergio Conc. (ng/ul)confirmed by Nanodrop 260/280 260/230
1. 2HFF p6 283.50 280.10 2.02 1.87
2. 218 HFF p7 586.30 446.10 2.05 2.00

September16, 2011, gDNA from Sergio, Salk Institute[edit]

Sample ID Conc. (ng/ul) by Sergio Conc. (ng/ul)confirmed by Nanodrop 260/280 260/230
1. H9 P43 mTeSR 62.00 62.80 1.89 0.99
2. H9 p43+Activin 100ng/mL 5days 90.80 90.80 1.85 0.70
3. H9 p43+BMP4 50ng/mL 5days 91.10 93.70 1.85 1.15
4. HUViPS4F1 p19 95.20 98.00 1.84 1.22
5. HUViPS4F1 p19+Activin 100ng/mL 5days 83.80 84.80 1.79 0.78
6. HUViPS4F1 p19+BMP4 50ng/mL 5days 80.00 78.60 1.84 0.96
7. HUViPS4F3 96.80 96.90 1.87 1.12
8. HUViPS4F3+Activin 100ng/mL 5days 90.20 91.90 1.78 0.80
9. HUViPS4F3+BMP4 50ng/mL 5days 80.20 80.60 1.86 0.96
  • Related lab note:
    • [[24]]
    • [[25]]
    • 330k BSPP capture of all of these samples were repeated again for PNAS revision (May2012):

September16, 2011, received 3 more gDNA from UPenn to repeat the capture of the samples with low QC values[edit]

Sample ID Conc. (ng/ul) by Sergio Conc. (ng/ul)confirmed by Nanodrop 260/280 260/230
1. KEBR028A 50.00 23.80 1.83 0.51
2. TZHZ031A 50.00 55.10 1.88 1.78
3. TZHZ041A 50.00 54.60 1.88 1.35

September 17, 2011, received 3 cell pellet samples from Alice (sample from Yang Xu's lab)[edit]

  • I extracted gDNA and elutee 150ul in elute1 and elute2. The concentration was was measure by Nanodrop.
Sample ID Conc. (ng/ul)confirmed by Nanodrop Volume (ul) Yields (ug) 260/280 260/230
1. Hues1 (elute1) 341.90 150.00 51.29 2.06 2.02
Hues1 (elute2) 64.00 150.00 9.60 2.04 2.07
2. Hues3 (elute1) 696.90 150.00 104.54 2.35 3.16
Hues3 (elute2) 183.90 150.00 27.59 2.10 2.08
3. Hues8 (elute1) 410.60 150.00 61.59 2.05 2.01
Hues8 (elute2) 125.00 150.00 18.75 2.07 2.04

December 13, 2011, received one sequencing library from Baylor, RC-1[edit]

  • RC-1 --> labeled conc. 70 ng/ul, volume ~ 8ul. I added 8ul of H2O to ncrease the volume, so the final conc. ~35ng/ul
  • This library was constructed using the same protocol as I did on the LC sciences's BSPP library. I performed qPCR with the barcode primers
  • Related lab note:
    • [[33]]
    • Re-amplified with library-free protocol: [[34]]
      • Summary of mapping data: [[35]]

March 1, 2012, received 6 gDNA samples (PGP1F hiPS) from Alice[edit]

Cap labeling Sample ID Lab ID Conc. (ng/ul) Passage
19 12.5-2x#1 2x#1 55.7 P5
20 12.5-1x#2 1x#2 68.1 P6
21 12.5-1x#3 1x#3 149.9 P5
22 12.5-2x#5 2x#5 34.5 P5
23 12.5-2x#6 2x#6 96.7 P5
24 12.5-1x#1 1x#1 114.6 P5
  • Related lab note:

April 15, 2012, Cell pellet samples from Sergio to Dinh[edit]

No. Sample ID Lab ID
hESC lines
1 HUES2 p41 Ap15-1
hiPSC lines:
2 ASThiPS4F1 p12 Ap15-2
3 ASThiPS4F2 p12 Ap15-3
Differentiate experiments:
4 HUES6 p39 Control TeSR Ap15-4
5 HUES6 p39 ACTIVIN Ap15-5
6 HUES6 p39 BMP4 Ap15-6
7 HUES9 p39 Control TeSR Ap15-7
8 HUES9 p39 ACTIVIN Ap15-8
9 HUES9 p39 BMP4 Ap15-9
10 HUES3 p36 Control TeSR Ap15-10
11 HUES3 p36 ACTIVIN Ap15-11
12 HUES3 p36 BMP4 Ap15-12
13 H1 p54 Control TeSR Ap15-13
14 H1 p54 ACTIVIN Ap15-14
15 ASThiPS4F5 p16 Control TeSR Ap15-15
16 ASThiPS4F5 p16 ACTIVIN Ap15-16
17 ASThiPS4F4 p36 Control TeSR Ap15-17
18 ASThiPS4F4 p36 ACTIVIN Ap15-18
19 ASThiPS4F4 p36 BMP4 Ap15-19

May 15, 2012, Cell pellet samples from Sergio to Dinh[edit]

No. Sample ID Lab ID
hESC lines:
1 H1 p48 Ma15-2
2 H9 p42 Ma15-3
3 HUES3 p33 Ma15-4
4 HUES6 p26 Ma15-5
5 HUES8 p35 Ma15-6
6 HUES9 p36 Ma15-7
iPSC lines:
7 ASThiPS4F3 p24 (derived from Astrocytes) Ma15-8
8 ASThiPS4F4 p16 (derived from Astrocytes) Ma15-9
9 FiPS4F2 p32 (derived from IMR90 fibroblasts) Ma15-10
10 FiPS4F5 p29 (derived from IMR90 fibroblasts) Ma15-11
11 KiPS4FA p54 (derived from keratinocytes) Ma15-12
12 Huv-iPS4F6 p23 (derived from HUVECs) Ma15-13
Somatic lines
13 IMR90 p6 Ma15-14
14 Keratinocytes p3 Ma15-15
Differentiation experiments:
15 H1 p47 Control Ma15-16
16 H1 p47 BMP-4 Ma15-17
17 ASThiPS4F5 p12 Control Ma15-18
18 ASThiPS4F5 p12 BMP-4 Ma15-19
19 Huv-iPS4F6 p23 Control Ma15-20
20 Huv-iPS4F6 p23 BMP-4 Ma15-21
21 Huv-iPS4F6 p23 ACTIVIN Ma15-1
Three samples below will not be captured with this batch
HUES2 p38
ASThiPS4F1 p8 (derived from Astrocytes)
ASThiPS4F2 p8 (derived from Astrocytes)

May 24, 2012, got more 8 gDNA for 330k BSPP capture from Anwesha (ASM and ASCM in human cells project, Harvard's group)[edit]

  • Note: All of gDNA, cDNA and ChIPed samples for this projected were stored by Alan.
  • For gDNA samples in the first batch, all of 8 samples have conc. of 38ng/ul and volume ~20ul
  • for the second batch, Anwesha sent total volume 40ul for each sample
Sample IDs Conc. (ng.ul) by Nanodrop
(from Harvard)
Amount (ug) in 40ul
GM gDNA 4-5-12 64.52 2.58
P10E3 gDNA 4-5-12 37.86 1.51
DF2 gDNA 4-5-12 70.00 2.80
H0 gDNA 4-5-12 84.52 3.38
H7 gDNA 4-5-12 184.33 7.37
H14 gDNA 4-5-12 167.18 6.69
H16 gDNA 4-5-12 120.60 4.82
  • Related labnote:
  • Mapping data: (not finished yet

August 22, 2012, got 2 gDNA and 3 cell pellet samples for 330k BSPP capture fromAlice (samples from Dr. Yang Xu)[edit]

No. SampleID LabIDs Nanodrop (ng/ul) A260 260/280 Yields (ug)
1 2-1C-8 AL-1 226.6 NA NA NA
2 3-5C-3 AL-2 375.5 NA NA NA
3 34HHP AL-3 256.8 5.136 2.08 51.4
4 34HHF_Y-53-A6 AL-4 142.1 2.842 2.04 28.4
5 34HHF_Y-53-B3 AL-5 140.1 2.802 2 28
  • Note: I got gDNA of sample ID AL-1 and AL-2 from Alice. Sample AL-3-5 as cell pellets.

August 22, 2012, Received 16 cell pellet (1x10^6 cells/tube) samples for 330k BSPP capture from Guanghui (Dr. Belmonte's lab)[edit]

No. Sample description Mark on the tube Lab ID Nanodrop (ng/ul) A260 260/280 Yields (ug)
1 WT-ESC H9-WT-ES GL-1 295.8 5.916 2.04 16.3
2 LRRK2-GS-ESC H9-LRRK-ES GL-2 220.6 4.412 2.07 12.1
3 WT-NSCs H9-WT-NSC-P9 GL-3 149.7 2.994 2.01 8.2
4 LRRK2-GS-NSCs H9-LRRK-NSC-P9 GL-4 172.3 3.445 2.06 9.5
5 2nd-iPSCs-WT#5 (early passage) H9-WT-NSC-iPSC#5 P18 GL-5 285.2 5.704 2.05 15.7
6 2nd-iPSCs-WT#3 (early passage) H9-WT-NSC-iPSC#3 P18 GL-6 296.6 5.932 2.03 16.3
7 2nd-iPSCs-LK2-GS#2 (early passage) H9-LRRK-NSC-iPSC#2 P18 GL-7 320.0 6.400 2.03 17.6
8 2nd-iPSCs-LK2-GS#6 (early passage) H9-LRRK-NSC-iPSC#6 P18 GL-8 339.3 6.786 2.04 18.7
9 2nd-iPSCs-WT#5 (late passage) W5-ips P34 GL-9 467.5 9.349 2.02 25.7
10 2nd-iPSCs-WT#3 (late passage) W2-ips P34 GL-10 431.7 8.633 2.01 23.7
11 2nd-iPSCs-LK2-G2#2 (late passage) L2-ips P34 GL-11 349.1 6.981 2.03 19.2
12 2nd-iPSCs-LK2-GS#6 (late passage) L6-ips P34 GL-12 234.5 4.691 2.04 12.9
13 Cardiomyocyes combine two tube to get 1M cells GL-13 72.2 1.445 1.89 4.0
14 WT-NSCs FA52-#6-NSC GL-14 137.3 2.747 2.01 7.6
15 FA-NSCs FA123#2-NSC GL-15 207.5 4.150 2.03 11.4
16 Corrected FA-NSCs FA-GC-16-NEO-NSC GL-16 135.5 2.710 2.00 7.5
  • Sample code GL1-GL13 for Project 1
  • Sample code GL14-GL16 for Project 2

June 12, 2013, received 32 gDNA samples (DNA methylation assay for Blueprint project)[edit]