Alice:Sample Record: Difference between revisions

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  received 9 tubes of PGP1F cell pellet (100,000 cells each) from:
  received 9 tubes of PGP1F cell pellet (100,000 cells each) from:
  Jay Lee
  Jay Lee
  WYSS Institute for Bio INS ENG
  WYSS Institute for Bio INS ENG

Revision as of 19:09, 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) 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, 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]