Alice:Sample Record: Difference between revisions
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[lane 3]: foreskin-lig: 14nM | [lane 3]: foreskin-lig: 14nM | ||
===August 14, 2009=== | ===August 14, 2009 (CV gDNA)=== | ||
We have received Craig Venter's ips and fibroblast | We have received Craig Venter's ips and fibroblast | ||
ips line 1st elution: 314ng/ul | ips line 1st elution: 314ng/ul | ||
Line 98: | Line 98: | ||
CV-ips: 26.3nM | CV-ips: 26.3nM | ||
CV-fibroblast: 10nM | CV-fibroblast: 10nM | ||
===January 27, 2010 (PGP1F cultured cell)=== | |||
received 9 tubes of PGP1F cell pellet (100,000 cells each) | |||
preformed DNA extraction on 1 tube [[http://genome-tech.ucsd.edu/LabNotes/index.php/Alice:LabNotes/2010-2-15 2-15-2010]] | |||
===February 11 , 2010 (CVF gDNA from Goldstein lab)=== | |||
picked up one tube of CVF (labeled as CVB, 0.19ug/ul) 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 | |||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''cell type''' | |||
| align="center" style="background:#f0f0f0;"|'''Patient #''' | |||
| align="center" style="background:#f0f0f0;"|'''Line''' | |||
| align="center" style="background:#f0f0f0;"|'''Age/sex''' | |||
| align="center" style="background:#f0f0f0;"|'''genotype''' | |||
| align="center" style="background:#f0f0f0;"|'''Reprograming factor''' | |||
| align="center" style="background:#f0f0f0;"|'''Passage #''' | |||
| align="center" style="background:#f0f0f0;"|'''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 [[http://genome-tech.ucsd.edu/LabNotes/index.php/Alice:LabNotes/2010-2-15 2-15-2010]] |
Revision as of 19:02, 17 February 2010
March 13, 2009
I prepared and sent out 2 tubes of Shotgun sequencing libraries to Dr.Billy Li through Fedex overnight. LabNote link [tube 1]: PGP1-CTRL, 48.5ng/ul, 30ul [tube 2]: PGP1-shaked, 46ng/ul, 30ul
May 25, 2009
Dr. Zhang and I each prepared 4 tubes of Shotgun sequencing libraries. A total of 8 tubes of solexa sequencing libraries were sent to BioGem. LabNote link, Dr. Zhang's notes [tube 1]: PGP1E0509k, 19nM, 40ul [tube 2]: PGP2E0509k, 20nM, 40ul [tube 3]: PGP3E0509k, 19nM, 40ul [tube 4]: NA12878E0509k, 33nM, 40ul [tube 5]: PGP2E0509A, 77nM, 40ul [tube 6]: PGP2E0509A, 64nM, 40ul [tube 7]: PGP2E0509A, 49.5nM, 40ul [tube 8]: NA12878E0509A, 60nM, 40ul
May 29, 2009
I prepared and sent out 2 tubes of sample for end-sequencing to Guao Yuan through Fedex overnight. LabNote link [tube 1]: PGP2_052909A, 111nM, 15ul [tube 2]: PGP3_052909A, 126nM, 15ul
June 4, 2009
I prepared and sent out 4 tubes of Shotgun sequencing libraries to BioGem. LabNote link [tube 1]: PGP5-1-060809, 62.5nM, 10ul, lane 4 [tube 2]: PGP5-2-060809, 65.7nM, 10ul, lane 5 [tube 3]: PGP7-1-060809, 75.5nM, 10ul, lane 6 [tube 4]: PGP7-2-060809, 79.7nM, 20ul, lane 7 and lane 8
June 10, 2009
I prepared and sent out 4 tubes of Shotgun sequencing libraries to Zhen Ye. LabNote link [tube 1]: PGP1-3-061009: 34nM x 15ul, lane 1 [tube 2]: PGP2-3-061009: 25nM x 15ul, lane 2 [tube 3]: PGP3-3-061009: 22nM x 15ul, lane 3 [tube 4]: NA12878-3-061009: 22nM x 15ul, lane 4
June 18, 2009
I prepared and sent out 4 tubes of Shotgun sequencing libraries to Zhen Ye. LabNote link [tube 1]: PGP5-1-060809, 62.5nM, 5ul [tube 2]: PGP5-2-060809, 65.7nM, 5ul [tube 3]: PGP7-1-060809, 75.5nM, 5ul
July 24, 2009
I prepared 1 tube of shotgun sequencing library (using Y-adaptor) and Alan sequenced it with our new machine. LabNote link [lane 3]: NA12878-072109: 50.5nM
July 28, 2009
The same library from last time is used to do sequencing on our new machine again. LabNote link [lane 4-7]: NA12878-072109: 50.5nM (loaded four times more than last time, which means actual concentration should be around 2.5ng/ul)
August 4, 2009
I prepared 5 tubes of shotgun sequencing libraries (using Y-adaptor) and Alan sequenced it with our new machine. LabNote link [lane 4]: NA12878: 88nM [lane 2]: foreskin: 70nM [lane 5]: Na12878-lig: 16nM [lane 1]: DF-lig: 10nM [lane 3]: foreskin-lig: 14nM
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)
August 13, 2009
I have prepared 2 tubes for end-sequencing. LabNote link lane 7: PGP2S-Phu 54.5nM lane 8: PGP2S-iProof 60.6nM
August 29, 2009
I prepared 6 tubes for shotgun sequencing. LabNote link lane 1: DF6-9-9 60nM lane 2: DF6-9-9 lane 3: foreskin 45nM lane 4: foreskin lane 5: PGP1-ips 38nM lane 6: CV-ips 90nM lane 7: CV-fibroblast 76nM lane 8: PGP1 34nM
Sptember 18, 2009
I prepared 4 tubes for shotgun sequencing. LabNote link DF6-9-9: 12.3nM foreskin: 5nM CV-ips: 26.3nM CV-fibroblast: 10nM
January 27, 2010 (PGP1F cultured cell)
received 9 tubes of PGP1F cell pellet (100,000 cells each)
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, 0.19ug/ul) 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]