Alice:Sample Record: Difference between revisions

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>Zsakura2
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  Div Medical Genetics DD2205 MCN
  Div Medical Genetics DD2205 MCN
  Nashville, TN 37232
  Nashville, TN 37232
*3/3/2010  Vanderbilt IPF familial DNA samples
{| {{table}}
{| {{table}}
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''ID #'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''ng/ul'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''260/280'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''260/230'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''volume per tube'''
|-
| ID #||ng/ul||260/280||260/230||volume per tube
|-
|-
| IPF 56JW525||65||1.86||1.38||80
| IPF 56JW525||65||1.86||1.38||80

Revision as of 21:46, 4 March 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, 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