Alice:Sample Record: Difference between revisions
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Tel. 858-453-4100, ext 1324 | Tel. 858-453-4100, ext 1324 | ||
{| {{table}} | {| {{table}} border=1 | ||
| align="center" style="background:#f0f0f0;"|'''Fibroblast couple''' | | align="center" style="background:#f0f0f0;"|'''Fibroblast couple''' | ||
| align="center" style="background:#f0f0f0;"|'''concentration (ug/ul)''' | | align="center" style="background:#f0f0f0;"|'''concentration (ug/ul)''' | ||
Line 800: | Line 800: | ||
=July 30, 2012 (Mouse iPS cell pellete from Yang Xu lab)= | =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)= | |||
{| {{table}} border=1 | |||
| align="center" style="background:#f0f0f0;"|'''Tube Number''' | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Concentration (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''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)= | |||
{| {{table}} border=1 | |||
| align="center" style="background:#f0f0f0;"|'''Tube Number''' | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Concentration (ug/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''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 (10ul @ 41ng/ul) : 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 | |||
Latest revision as of 17:06, 12 November 2015
August 14, 2009 (CV gDNA)[edit]
- received genomic DNA samples extracted from Craig Venter's skin fibroblast cells and its iPSCs:
Sample ID | concentration (ng/ul) | Note |
ips line 1st elution | 314 | |
ips line 2nd elution | 127 | (took out 30ul + 30ul ddH2O: 68ng/ul) |
fibroblast 1st elution | 578 | |
fibroblast 2nd elution | 476.8 | (took out 30ul + 30ul ddH2O: 272.9ng/ul) |
January 27, 2010 (PGP1F cultured cell)[edit]
- received 9 tubes of PGP1F cell pellet (100,000 cells each) from:
- Jay Lee
- WYSS Institute for Bio INS ENG
- 4 Blackfan Cir HIM 1040
- Boston, MA 02115-5713
- preformed DNA extraction on 1 tube [2-15-2010 Labnote]
February 11 , 2010 (CVF gDNA from Goldstein lab)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
- received 4 tubes of CV samples from Jessica Young(Goldstein lab): CV1, CV2, CV3, CV4
May 4, 2010 (gDNA from Salk)[edit]
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
Fibroblast couple | concentration (ug/ul) | volume (ul) | passage number | |
HFF XF (Human Foreskin fibroblast Xeno free) | 0.2 | 50 | 9 | |
FiPS 3F #1 | 0.178 | 56 | 24 | |
keratinocyte couple | ||||
Keratinocyte MMTA (human foreskin keratinocytes MMTA) | 0.5 | 20 | 5 | |
KiPS 4F #8 | 0.42 | 23.8 | 28 | |
Astrocytes | ||||
human astrocytes | 0.36 | 90 | 12 | |
ASTiPS4F-4 | 0.51 | 90 | 10 | |
ASTiPS4F-5 | 0.71 | 90 | 10 | |
HUVEC | ||||
Human HUVEC | 1.12 | 90 | 2 | |
HUViPS4F-1 | 1.03 | 90 | 10 | |
HUViPS4F-3 | 0.47 | 90 | 15 | |
- 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
- HFF XF, FiPS 3F #1
- Human HUVEC, HUViPS4F-1, HUViPS4F-3
- Keratinocyte MMTA and KiPS 4F #8
- 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)[edit]
- 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)[edit]
- 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)[edit]
- input DNA amount was 3ug
- dHiF, ips dHif#8, ips dHif#9
- H9 ES, BG01 ES
June 23, 2010 (cell pellete from Daley lab)[edit]
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)[edit]
- 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)[edit]
- 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)[edit]
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)[edit]
- 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)[edit]
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)[edit]
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)[edit]
- 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)[edit]
- 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)[edit]
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)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
e7 A#1: 1239.5ng/ul e7 B#1: 1291.2ng/ul e7 5#4: 981.9ng/ul HFF1013: 709ng/ul Detailed sample information from Sergio: Sample 1: A#1 Flag-Oct4-HASox2-Klf4-cMyc (OS-KM) Sample 4: B#1 FlagOct4vP16-HASox2-Klf4 –cMyc (OvP16S-KM) Sample 9: 5#4 FlagOct4vP16-HASox2 (OvP16Sox2) Sample 14: 10/03 starting population
March 10, 2011 (cell pelletes from GuangHui, SALK Belmonte Lab)[edit]
~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)[edit]
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)
May 27, 2011 (gDNA from NYSCF)[edit]
- Daniel Paull
- New York Stem Cell Foundation
- 3960 Broadway, room 450D
- New York, NY 10032
Tube Number Sample Name (Passage Number) Volume Amount of DNA 1 H2 (P9) 8.1 µl 5 µg 2 H2 Oocyte Donor DNA (N/A) 44 µl 5 µg 3 1016A iPS (P8) 9 µl 5 µg 4 1016 Somatic Cell (P10) 45 µl 4.7 µg 5 pES1 (P8) 5.6 µl 5 µg 6 1034B iPS (P6) 7.1 µl 5 µg
June 3, 2011 (cell pellet from Yang Xu lab)[edit]
- Tongbiao dropped off six samples
218HFF P7 DF DF 4-1-37 218HFF4-11 DF 4-1-48 218 HFF2-11
June 10, 2011 (gDNA from Goldstein Lab)[edit]
- Picked up 8 samples from Jessica Young
CVB P14 mix: 179ng/ul CVB 1.7: 83ng/ul CVB 1.8: 50ng/ul CVB 1.9: 93.2ng/ul CVI P14 mix: 141.4ng/ul CVI 1.13: 125ng/ul CVI 1.14: 129ng/ul CVI 1.15: 84.2ng/ul
August 16, 2011 (mouse gDNA from PKU, China)[edit]
- Dr. Zhang brought back 5 mouse gDNA samples with 180ul each (mouse ES lines reprogrammed by somatic nuclear transfer)
B6(1)MEF P3: 171.8ng/ul B6(2)MEF P3: 94.6ng/ul ntES A P8: 321.7ng/ul ntES B P8: 313.8ng/ul ntES C P7: 237.7ng/ul
August 22, 2011 (gDNA from Goldstein lab)[edit]
- Athurva picked up 4 Hues9 samples from Goldstein lab
Hues 9 1.7: 186.6ng/ul Hues 9 1.8: 138.1ng/ul Hues 9 1.9: 106.5ng/ul Hues 9 mixed: 104.4ng/ul (note: 260/280 ratio is 1.69)
September 17, 2011 (cell pellets from Yang Xu lab)[edit]
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)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
- 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)[edit]
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)[edit]
Hues9 p14 DNA
June 19, 2012 (gDNA from Jessica, Dr. Larry Goldstein lab)[edit]
- 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)[edit]
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)[edit]
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)[edit]
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)[edit]
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)[edit]
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)[edit]
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 (10ul @ 41ng/ul) : 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