Alice:Sample Record: Difference between revisions
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**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 [[http://genome-tech.ucsd.edu/LabNotes/index.php/Alice:LabNotes/2010-6-25 labnote]] | **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 [[http://genome-tech.ucsd.edu/LabNotes/index.php/Alice:LabNotes/2010-6-25 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 (gDNA from Sergio, samples were shipped from Barcelona)= | =June 29, 2010 (gDNA from Sergio, samples were shipped from Barcelona)= |
Revision as of 17:49, 12 July 2010
August 14, 2009 (CV gDNA)
- We have received Craig Venter's ips and fibroblast:
- ips line 1st elution: 314ng/ul
- ips line 2nd elution: 127ng/ul (took out 30ul + 30ul ddH2O: 68ng/ul)
- fibroblast 1st elution: 578ng/ul
- fibroblast 2nd elution: 476.8ng/ul (took out 30ul + 30ul ddH2O: 272.9ng/ul)
January 27, 2010 (PGP1F cultured cell)
- 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]
February 11 , 2010 (CVF gDNA from Goldstein lab)
- 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 Harvrd)
- 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 (more CV gDNA)
- 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
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 |
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 (gDNA from Sergio, 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