picked up one tube of CVF (labeled as CVB, passage 13 fibroblast, 0.19ug/ul, ~100ul) from Jessica Young (Goldstein lab) in Leitchtag building
February 11, 2010 (gDNA from Eggan lab)
received 8 gDNA samples and 1 cell pellet from:
Evangelos Kiskinis
Harvard University
7 Divinity Avenue
Fairchild Biochemistry, Eggan Lab
Cambridge, MA 02138
cell type
Patient #
Line
Age/sex
genotype
Reprograming factor
Passage #
DNA (ng/ul)
hFib
17
17
71/F
WT
-
7
2000
ips
17
17a
71/F
WT
OCt4/Sox2/Klf4
20
447
ips
17
17b
71/F
WT
OCt4/Sox2/Klf4
23
2600
hFib
11
11
36/M
WT
-
7
2000
ips
11
11a
36/M
WT
OCt4/Sox2/Klf4
24
1037
ips
11
11b
36/M
WT
OCt4/Sox2/Klf4
20
1612
hFib
29
29
29/F
SOD1L144F
-
8
400
ips
29
29e
29/F
SOD1L144F
OCt4/Sox2/Klf4
21
cell pellet
ips
29
29A
29/F
SOD1L144F
Oct4/Sox2/Klf4/cMYC
36
1200
preformed DNA extraction on ips 29e p21 [2-15-2010]
February 26, 2010 (sequencing libraries from Georgia)
The samples were sent on 2/25/2010 through Fedex from:
Lynda Abernathy-Shi Lab
Medical College of Georgia
1120 15th Street
Augusta, GA 30912
Sample ID
Size
concentration (ng/ul)
Total Volume (ul)
EJ644
250-350bp
10
18
EJ645
250-350bp
10
15
EJ656
250-350bp
3.6
17
EJ657
250-350bp
3.2
20
March 2, 2010 (gDNA from Harvard)
received two tubes of sample from Jay Lee (Harvard):
CD1 PGP1 ips P16: 399ng/ul x 200ul
PGP1F 80 gDNA: 299ng/ul x 200ul
March 4, 2010 (gDNA from Vanderbilt)
received 10 samples from Vanderbilt Med Center:
Joy Cogan, 615-322-7601
Vanderbilt Med Center
Div Medical Genetics DD2205 MCN
Nashville, TN 37232
3/3/2010 Vanderbilt IPF familial DNA samples
ID #
ng/ul
260/280
260/230
volume per tube
IPF 56JW525
65
1.86
1.38
80
IPF 56WW608
60
1.9
1.66
100
IPF 121BP1349
105
1.93
1.13
55
IPF 121DB1353
148
1.89
1.47
40
IPF 125DC1384
67
1.91
1.18
75
IPF 125GA1382
107
1.91
1.49
47
IPF 134GH1580
73
2.03
0.83
75
IPF 134LM1450
68
1.93
1.2
80
IPF 139JS1477
92
1.3
1.04
55
IPF 139TD1515
51
2.01
0.73
120
March 30, 2010 (CV gDNA from Goldstein lab)
received 4 tubes of CV samples from Jessica Young(Goldstein lab): CV1, CV2, CV3, CV4
May 4, 2010 (gDNA from Salk)
Sergio Ruiz Macías, PhD
Gene Expression Lab (GEL-B)
Stem Cell Facility
The Salk Institute For Biological Studies
10010 North Torrey Pines Road
92037 La Jolla, CA, USA
sruiz@salk.edu
Tel. 858-453-4100, ext 1324
genomic DNA was extracted using the QIAmp DNA Mini and Blood Extraction Kit from Qiagen. DNA is resuspended in AE buffer (10mM Tris Cl; 0.5mM EDTA)
priority:
Keratinocyte MMTA and KiPS 4F #8
Human HUVEC, HUViPS4F-1, HUViPS4F-3
HFF XF, FiPS 3F #1
human astrocytes, ASTiPS4F-4, ASTiPS4F-5
NOTE:
HUVEC samples had very low concentration after shearing and end-repair reactions. Thus we suspect the DNA concentration that Sergio has given might not be accurate, and we measured the concentration again with Nanodrop and Qubit.
Sample ID
Nanodrop result (ng/ul)
Qubit result (ng/ul)
Average (ng/ul)
HUVEC
46.4
27.7
37.05
HUV ips4F1
79.5
54
66.75
HUV ips4F3
34.4
25.9
30.15
Measured the concentration of Astrocyte sets again, because the library construction results seemed to be problematic (see labnotes 8-7-2010)
Sample ID
concentration (ng/ul)
Ast
23
Ast iPS 4F4
37.4
Ast iPS 4F5
51
June 14, 2010 (more gDNA from Salk)
cells were reprogrammed and collected by Sergio Ruiz Macías, PhD
more HUVEC samples:
green = remaining gDNA from the last batch (same passage #, etc.)
blue = newly cultured cells from HUVEC lines (more passage #)
June 15, 2010 (cell pelletes from Wisconsin)
received two cell pelletes that was prepared by Jessica E. Antosiewicz-Bourget
FedEx copy:
Mitch Probasco
Biotech Center
425 Henry Mall
Madison, WI 53706
phone: 6088900175
DF19.11b p34 ~10^7 cells (06-07-10)
ips4.7 p36 ~10^7 cells (06-11-10)
June 16, 2010 (sheared gDNA from Daley lab)
input DNA amount was 3ug
dHiF, ips dHif#8, ips dHif#9
H9 ES, BG01 ES
June 23, 2010 (cell pellete from Daley lab)
Philip Manos
Children's Hospital / Stem Cell Program
1 Blackfan Cir
Boston; MA 02115-5713
CF Fib
CF Rips 1.4
CF Rips 1.9
BJ1 1.1
BJ1-Rips 1.2; p5 3/30
BJ1 Fibro
BJ Fibro
June 25, 2010 (more cell pellete from Daley lab)
two more tubes of CF Fib cell pelletes since the DNA extraction yield was very low last time
The yield for one of the tube for this batch is still very low (smiliar to the results from last time, for detailed information, please check out [labnote]
June 25, 2010 (gDNA from Jay Lee)
five tubes of gDNA for Sanger confirmation (500ng each)
dHif Fib
dHif ips 8
dHif ips 9
H9 ES
BG01 ES
June 29, 2010 (more gDNA from Salk, samples were shipped from Barcelona)
sample ID
Passage #
amount of DNA total
concentration
Note
HNSC
13.4ug
66.99ng/ul
Human Neural Stem cells
hNips2F
23
53.6ug
26875ng/ul
grown on matrigel; Couple Neural stem cells/hNiPS
hFips 4F-7
9
31.2ug
156.37ng/ul
grown on matrigel; another line made from the HFF xF fibroblast
hKips 3F-7
24
10ug
32.84ng/ul
grown on matrigel; another line made from the human foreskin keratinocytes MMTA
July 1, 2010 (gDNA from Daley and Jay Lee)
H1 p39 (500ng of gDNA and 3ug of sheared gDNA for library construction)
PGP1F 8 gDNA ~25ug total
July 13, 2010 (gDNA for CV Fib colonal lines from Jessica, Goldstein lab)
Sample ID
concentration (ng/ul)
Note
CV9
41
(95ul DNA total)
CV10
67.5
(90ul DNA total)
CV11
32.9
(95ul DNA total)
CV12
56.5
(90ul DNA total)
CV13
12.8
(48ul DNA total)
October 24, 2010 (cell pellete from TongBiao Zhao, Xu Lab)
HFF P5 (two tubes, each with ~1 million cells)
38H1C 6 P10 (two tubes, each with ~ half million cells)
November 1, 2010 (more gDNA from Salk, Belmonte group)
received 7 samples from Sergio, measured the concentration of these 7 samples with Nanodrop (blanked with AE)
Sample
concentration (ng/ul)
FiPS F-2 P40
75.6
FiPS F-2 P9
109.6
FiPS 4F5 P44
90.5
FiPS 4F5 P15
94.8
Plvthm Rb4-D P10
45.6
Plvtuhm Rb4-5 P10
119.1
IMR90 P4
36.2
November 12, 2010 (gDNA from Salk)
received 5 tubes of sample from Sergio (added 50ul of ddH2O to the first four tubes below to get higher volume for easier pipetting purpose, then measured their concentration with Nanodrop)
Sample ID
concentration
MSCiPS #8 P14
105.4ng/ul
MSCiPS #4 P14
181.4ng/ul
1F iPS
28.6ng/ul
KiPS3F7 P29
43ng/ul
aMSCs p7
184.8ng/ul
November 22, 2010 (gDNA from Salk)
Sample
Total DNA amount
Olf MSC*
19µg
CD34+ hematopoietic progenitors from Olf MSC
4.5µg
Kips+
12.6µg
CD34+ hematopoietic progenitors from Kips
4.1µg
received additional tube of Ast4F4 from Sergio on 11-23-2010 to do mutation validation on this line again
December 7, 2010 (gDNA from UPenn-----methylome)
received 48 African genomic DNA samples for DMR capture from
Tishkoff Lab - Dept of Genetics
University of Pennsylvania
430 Clinical Research Building
415 Curie Blvd
Philadelphia, PA 19104-6145
LabID
1M sample #
'
'
'
15ug vol ng
80ng/ul total Vol ul
Diluant Vol ul
'
Well
Volume ul
Conc ng/ul approx
CAPB016
76.00
187.5
111.5
A01
50
100
CAPB046
92.00
187.5
95.5
B01
50
100
CAPB056a
71.00
187.5
116.5
C01
50
100
CAPL056
78.00
187.5
109.5
D01
50
100
CAPM007
94.00
187.5
93.5
E01
50
100
TZHZ018A
160.00
187.5
27.5
F01
50
100
TZHZ033B
128.00
187.5
59.5
G01
50
100
TZHZ075A
257.00
187.5
-69.5
H01
50
100
TZHZ214
133.00
187.5
54.5
A02
50
100
TZHZ221B
154.00
187.5
33.5
B02
50
100
TZSW067
224.00
187.5
-36.5
C02
50
100
TZSW128B
103.00
187.5
84.5
D02
50
100
TZSW131A
123.00
187.5
64.5
E02
50
100
TZSW132B
259.00
187.5
-71.5
F02
50
100
TZSW135B
321.00
187.5
-133.5
G02
50
100
CAMF013A
156.7
125
0
H02
50
100
CAFU043
89.3
125
35.7
A03
50
100
CAFU042
113.6
125
11.4
B03
50
100
CAFU028
93.8
125
31.2
C03
50
100
CAMF022A
94.3
125
30.7
D03
50
100
CAPB043
41.8
125
83.2
E03
50
100
CAPL049
91.5
125
33.5
F03
50
100
CAPM001A
89.8
125
35.2
G03
50
100
CAPL036
126.1
125
0
H03
50
100
KEBR007A
124
125
1
A04
50
100
KEBR028A
78.5
125
46.5
B04
50
100
KEBR042B
190.8
125
0
C04
50
100
KEBR040A
184.7
125
0
D04
50
100
KEBR061A
55.6
125
69.4
E04
50
100
KEPK003A
102
125
23
F04
50
100
KEPK006A
80.6
125
44.4
G04
50
100
KEPK007A
130.4
125
0
H04
50
100
KEPK010A
82.4
125
42.6
A05
50
100
KEPK016A
112.8
125
12.2
B05
50
100
CAPM047
son
120.2
C05
50
100
CAPM003A
parent
237.8
D05
50
100
CAPM004A
parent
139
E05
50
100
CAPM056A
daughter
196.2
F05
50
100
ETAM042
M
Yes
No
Yes
17.4
G05
50
100
ETAM071
M
Yes
No
Yes
17.4
H05
50
100
ETAM077
M
Yes
No
Yes
17.4
A06
50
100
ETAM058
M
Yes
No
Yes
17.9
B06
50
100
ETAM065
M
Yes
No
Yes
17.9
C06
50
100
ETSB008
18
F
Yes
Yes
Yes
HEADACHE; ABDOMINAL CRAMP; INTESTINAL PARASITE
D06
50
100
ETSB027
19
M
Yes
Yes
Yes
NA
E06
50
100
ETSB031
30
M
Yes
Yes
Yes
2 WKS BACK INTESTINAL PARASITE AND HEADACHE
F06
50
100
ETSB035
19
M
Yes
Yes
Yes
HEADACHE
G06
50
100
ETSB036
20
F
Yes
Yes
Yes
NA
H06
50
100
December 10, 2010 (gDNA from Johns Hopkins-----methylome)
recevied 48 genomic DNA samples for DMR capture from
Fedex Label:
Eirikur Briem
Johns Hopkins University
855 N. Wolfe Stree
Rangos, 580.14
Baltimore, MD 21205
Final Volume (uL)
Final_Conc (ng/uL)
Sample_ID
Kun_Well
50
30
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
30
50
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
January 7, 2011 (cell pelletes from TongBiao, Xu Lab)
3 cell pelletes were received (1-3 million cells each)
2HFF P6
2HFF 8d-10
2HFF 7-10 3M
January 26, 2011 (mouse cell pelletes from TongBiao, Xu Lab)
3 cell pelletes were received (1-3 million cells each)
1E12 P20 (1.5 million cells collected)
2eiPS 2-p3 (12-7-2009; 2 million cells collected)---very low yield after DNA extraction
B6-MEF P0-3 (3 million cells collected)
NOTE: Picked up another batch of sample for 2eiPS 2-p5 (12-10-2009) on 1/31/2011;
Previous sample 2eiPS 2-P3 had very little yield after DNA extraction (see labnote 1-28-2011),
possibly because small amount of cells were collected
March 9, 2011 (gDNA from Sergio, SALK Belmonte Lab)
March 10, 2011 (cell pelletes from GuangHui, SALK Belmonte Lab)
~1 million cells were collected per sample
DNA extraction done on 3/10/2011 with Noi, elute in 300ul AE:
HGPS: 75.7 ng/ul
cHGPS1: 57.1ng/ul
cHGPS40: 100.2ng/ul
AWS: 42.2ng/ul
cAWS1: 130ng/ul
NOTE: second batch of sample HGPS (~1 million cells collected) is received on March 31, 2011
Because the sequencing results and repeated library construction didn't work for the first batch, therefore Guanghui dropped off the second batch instead
May 16, 2011 (gDNA from Sergio, SALK Belmonte lab)
Sample 3: e7 A#4 (OS-KM)
Sample 5: e7 B#2 (OvP16S-KM)
Sample 11: e7 5#9 (OvP16Sox2)
The progenitor cell line for these iPS cells was received on 3/9/2011 (HFF1013)
September 17, 2011 (cell pellets from Yang Xu lab)
3 of them are Human ES cells for methylation studies
Hues 1
Hues 3
Hues 8
3 of them are iPS cells for exome sequencing
33 HFF
331C 12-8
331C 8-10
December 15, 2011 (gDNA from NYSCF, Dieter lab)
Athurva received these samples in early December and passed them to me on 12/6/2011
stem cells:
pES 5: 38ng/ul
pES 4: 142ng/ul
pES 3: 39ng/ul
pES 1: 68ng/ul
stem cells reprogrammed using somatic nuclear transfer:
H6: 100ng/ul
H5: 80ng/ul
H4: 270ng/ul
H3: 95ng/ul
cells for reference:
1083: 485ng/ul
1082: 186ng/ul
1058: 18ng/ul
December 15, 2011 (mouse cell pellets and gDNA from Yang Xu lab)
Tongbiao passed these samples to me in late November 2011
these are 4 independent clones derived from B6 fibroblast using SCNT
mouse cells reprogrammed using nuclear transfer:
ntES #D p8 mice (extracted gDNA and first elution yielded 200ul with 144.8ng/ul)
ntES #F p8 mice (extracted gDNA and first elution yielded 200ul with 157.9ng/ul)
NB 1: about 2x10^6 cells, yield: 363.2ng/ul
NB 3: about 2x10^6 cells, yield: 407.9ng/ul
February 3, 2012 (human iPSC and mouse NT cell pellets from Yang Xu lab)
Tongbiao prepared 10 mouse NT samples and Zhen Ning prepared 5 human iPSCs:
Human cells:
parental line: HHF
four iPSC line: B-C-5, 1-9, B-1-9 and B-1-20
Mouse cells:
parental line: B6-P1-2-MEF
NT line: B6, B7, B8, B9, B10, B11, B12, B13, B14
February 6, 2012 (more human iPSCs from Yang Xu lab)
Tongbiao prepared 3 human iPSCs:
parental: 34HHF
iPSCs: 34HHF2-1c-8, 34HHF3-5c-3
April 30, 2012 (human iPSCs and Mouse SCNT from Yang Xu lab)
human lines:
Y1, Y2, Y4, Y7, Y8, Y9, Y16 (progenitor is HHF, previously sequenced in the last Hi-Seq run, samples received on 3/27/2012)
A4, A6, A20, B3, B18 (progenitor is 34HHF, previously sequenced in the last Hi-Seq run)
*Puma+P21 knock out and episomal
1EDKD-2
1EDKD-3
2EDKD-1
2EDKD-3
2EDKD-6
3EDKD-4
4EDKD-3
(the first number indicates the experiment; E=episomal; DKD=double knockdown of Puma/p21; the final number indicates the clone/colony)
mouse lines:
2A4F1, 2A4F33, (progenitor is B6MEF, previously sequenced? received on 3/27/2012)
B6-P1-1 (progenitor for two previous NTSC sample: NB1 and NB3)
(B7-B13 were recovered from pelletes collected and frozen down in China)
SCNT B7 P2
SCNT B8 P2
SCNT B9 P2
SCNT B10 P2
SCNT B11 P2
SCNT B12 P2
SCNT B13 P2
B14 (recovered from pelletes frozen down by TongBiao)
(progenitor is previously sequenced B6-p1-2 in the last Hi-Seq run)
May 10, 2012 (gDNA from Harvard, received by Jessica at Dr. Larry Goldstein lab)
Hues9 p14 DNA
June 19, 2012 (gDNA from Jessica, Dr. Larry Goldstein lab)
TALEN iPSC lines generated from CV-B iPSC lines
Sample Name Concentration (total volume is 100ul)
IIA12 549.2 ng/ul
IIA11 242.2 ng/ul
IIF12 171.2 ng/ul 2nd tube is: 57.0 ng/ul
IIB7 196.2 ng/ul 2nd tube is: 55.8 ng/ul
IIB12 183 ng/ul 2nd tube is: 66.6 ng/ul
IID12 578 ng/ul
July 30, 2012 (Mouse iPS cell pellete from Yang Xu lab)
B6-P1-2 (progenitor B6 MEF for previous batch of SCNT samples)
miPS-B6-4-D8
miPS-B6-4-D3
miPS-B4-4-D1
miPS-B6-4-B3
human samples for exome and methylation analysis:
34HHF
A6
B3
3-5C-3
2-1C-8
September 14, 2012 (human SCNT gDNA from NYSCF)
Tube Number
Sample
Concentration (ng/ul)
Volume (ul)
Total amount (ug)
1
1110
121.9
23
2.8
2
swaPS3
546.3
9.15
5
3
1105
303.4
16.48
5
4
pES6
599.6
8.34
5
5
1043
369.4
13.54
5
6
pES2
1142
4.38
5
7
1058
303.8
16.46
5
October 9, 2012 (mouse iPSCs samples from PKU)
Tube Number
Sample
Concentration (ug/ul)
Volume (ul)
1
MEF (long term)
10
-
2
created MEF
10
-
6
C2 clone
10
-
7
starting MEF
10
-
8
C3 clone
10
-
September 1, 2013 (mouse B6MEF from Xu lab)
B6MEF 1- P3 (progenitor of miPS B3, D1, D3, D8)
frozen cell pellet of 10cm plate, roughly few million cells
DNA extraction result: 89 ng/ul, 260/180: 2.0
January 8, 2014 (human gDNA from Linzhao Cheng lab in Johns Hopkins Medical center)
BC1 cells targeting the AAVS1 locus by either TALEN or Cas9-gRNA. All of the samples are ~200ng/ul in 40ul
1) BC1 p 16+14 (parental)
2) BC1 p16+21 (control)
3) BC1 AAV GFP TALEN c3 p16+21
4) BC1 AAV GFP TALEN c6 p16+21
5) BC1 AAV GFP hCas9 c4 p16+21
6) BC1 AAV GFP hCas9 c16 p16+21
October 20, 2015 (mouse gDNA from Keiichiro Suzuki in Belmonte Lab at Salk)
CRISPR mediated knock-in at Rosa26 transgenic mice(mCherry+) into non-dividing cells (injected into muscle cells)
Kei sample 3 (~4500 cells): +Cas9 mCherry+ gDNA
Kei sample 4 (~1500 cells): -Cas9 mCherry+ gDNA
Kei sample 6 (320 cells): +Cas9 GFP+ gDNA
Kei sample: LAM-PCR product +cas9 GFP+ PCR amplicon (~150bp correct band, and another band at ~180bp);
amplicon goes from upstream of knock-in site on gDNA and extends to beginning of GFP