Contents
1 2014 sample tracking
2 November5, 2010 (Mouse gDNA from La Spada's lab, UCSD)
3 December 7, 2010 (Sarah's African gDNA, UPenn )
4 December 10, 2010 (normal/tumor gDNA from JHU)
5 December 16, 2010 (Bisulfite converted mouse gDNA from JHU)
6 February 2, 2011 (Brain gDNA of Parkinson's patients from Burnham Institute, human frozen cerebral cortex)
7 March 10, 2011, Cell pellet samples from Belmonte's lab, Salk Institute
8 April 21, 2011, PGP1 iPS gDNA from Harvard
9 April 27, 2011, gDNA of TET study from Harvard Medical School
10 May 19, 2011, gDNA from the blood samples of HIV patients, UCSD Medical School
11 May 25, 2011, gDNA of 10 different tissues from Billi Li, Standforf Univ
12 July 8, 2011, gDNA from the blood samples of control and GA patients from Kang Zhang's lab, UCSD
13 July 29, 2011, gDNA of 3 human iPS lines with single nonsynonymous mutations, UCSD
14 August 1, 2011, gDNA of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA
15 August25, 2011, gDNA from fibroblast cells that are the somatic line of the three single nonsynonymous mutation iPS on the record of July29, 2011
16 September16, 2011, gDNA from Sergio, Salk Institute
17 September16, 2011, received 3 more gDNA from UPenn to repeat the capture of the samples with low QC values
18 September 17, 2011, received 3 cell pellet samples from Alice (sample from Yang Xu's lab)
19 December 13, 2011, received one sequencing library from Baylor, RC-1
20 March 1, 2012, received 6 gDNA samples (PGP1F hiPS) from Alice
21 April 15, 2012, Cell pellet samples from Sergio to Dinh
22 May 15, 2012, Cell pellet samples from Sergio to Dinh
23 May 24, 2012, got more 8 gDNA for 330k BSPP capture from Anwesha (ASM and ASCM in human cells project, Harvard's group)
24 August 22, 2012, got 2 gDNA and 3 cell pellet samples for 330k BSPP capture fromAlice (samples from Dr. Yang Xu)
25 August 22, 2012, Received 16 cell pellet (1x10^6 cells/tube) samples for 330k BSPP capture from Guanghui (Dr. Belmonte's lab)
26 June 12, 2013, received 32 gDNA samples (DNA methylation assay for Blueprint project)
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
aliquot 21ul out of 50ul samples into another 96-well plate
Related lab note:
Data analysis:
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
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 ]