Alice:LabNotes/2009-7-6: Difference between revisions

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>Jie deng
(New page: Sent out the following tubes for Covaris shearing to Dr. Billy Li (Harvard) PGP1_070809: 25ul (13ng/ul) PGP2_070809: 30ul (9.7ng/ul) PGP3_070809: 32ul (8.4ng/ul) NA12878_070809: 2...)
 
>Jie deng
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  The detailed capture reaction setup can be found under LabNotes 6/28/09
Pooled all the captured product based on the following table:
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''sample'''
| align="center" style="background:#f0f0f0;"|'''a1'''
| align="center" style="background:#f0f0f0;"|'''a2'''
| align="center" style="background:#f0f0f0;"|'''a3'''
| align="center" style="background:#f0f0f0;"|'''a4'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''b1'''
| align="center" style="background:#f0f0f0;"|'''b2'''
| align="center" style="background:#f0f0f0;"|'''b3'''
| align="center" style="background:#f0f0f0;"|'''b4'''
|-
| concentration (ng/ul)||16||9.7||6.7||12.3||||9.4||7.6||5.1||9.8
|-
| volume (ul)||10||8.2||17||9.5||||15||9.3||20||10.5
|-
| total (ng)||160||80||115.2||116.8||||141||70.5||101.5||103
|-
|
|}


  Sent out the following tubes for Covaris shearing to Dr. Billy Li (Harvard)  
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''sample'''
| align="center" style="background:#f0f0f0;"|'''c1'''
| align="center" style="background:#f0f0f0;"|'''c2'''
| align="center" style="background:#f0f0f0;"|'''c3'''
| align="center" style="background:#f0f0f0;"|'''c4'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''d1'''
| align="center" style="background:#f0f0f0;"|'''d2'''
| align="center" style="background:#f0f0f0;"|'''d3'''
| align="center" style="background:#f0f0f0;"|'''d4'''
|-
| concentration (ng/ul)||13||7.2||4.9||5.4||||14||7.8||6.6||7.4
|-
| volume (ul)||10||9||19||17.5||||10||9||15||14
|-
| total (ng)||130||65||93.6||95||||140||70||100.8||102.2
|-
|
|}
 
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''sample'''
| align="center" style="background:#f0f0f0;"|'''e1'''
| align="center" style="background:#f0f0f0;"|'''e2'''
| align="center" style="background:#f0f0f0;"|'''e3'''
| align="center" style="background:#f0f0f0;"|'''e4'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''f1'''
| align="center" style="background:#f0f0f0;"|'''f2'''
| align="center" style="background:#f0f0f0;"|'''f3'''
| align="center" style="background:#f0f0f0;"|'''f4'''
|-
| concentration (ng/ul)||11||3.1||3.4||4.7||||9.5||5.5||2.2||4.6
|-
| volume (ul)||7.3||13||17||12.5||||2.9||2.5||9||4.4
|-
| total (ng)||80.3||40.15||57.8||58.6||||27.5||13.8||19.8||20
|-
|
|}
 
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''sample'''
| align="center" style="background:#f0f0f0;"|'''DF1'''
| align="center" style="background:#f0f0f0;"|'''DF2'''
| align="center" style="background:#f0f0f0;"|'''DF3'''
| align="center" style="background:#f0f0f0;"|'''DF4'''
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''FS1'''
| align="center" style="background:#f0f0f0;"|'''FS2'''
| align="center" style="background:#f0f0f0;"|'''FS3'''
| align="center" style="background:#f0f0f0;"|'''FS4'''
|-
| concentration (ng/ul)||17.7||10.1||6.2||11.7||||15.3||4.1||5.4||5.2
|-
| volume (ul)||9.2||8.1||19||10.2||||8.6||16||18||18.5
|-
| total (ng)||163.6||81.8||117.8||119.4||||131.8||65.9||95||111.7
|-
|
|}
 
perform E-gel size selection after pooling all the samples together (8 total):
assume 70% recovery rate, the total amount of DNA in each sample set is:
PGP1_070809: 25ul (330.4ng)
PGP2_070809: 30ul (291ng)
PGP3_070809: 32ul (269ng)
NA12878_070809: 26ul (289ng)
PGP5_070809: 31ul (166ng)
PGP7_070809: 17ul (65ng)
DF6-9-9_070809: 33ul (177ng)
foreskin_070809: 44ul (283ng)
Since PGP7 had very little amount of DNA, it was not send out for shearing. And I will need to repeat the capture on sample f3.
 
  Sent out the following tubes for Covaris shearing to Dr. Billy Li (Harvard) on 7/8/09
  PGP1_070809: 25ul (13ng/ul)
  PGP1_070809: 25ul (13ng/ul)
  PGP2_070809: 30ul (9.7ng/ul)
  PGP2_070809: 30ul (9.7ng/ul)

Latest revision as of 01:37, 13 July 2009

The detailed capture reaction setup can be found under LabNotes 6/28/09
Pooled all the captured product based on the following table:
sample a1 a2 a3 a4 ' b1 b2 b3 b4
concentration (ng/ul) 16 9.7 6.7 12.3 9.4 7.6 5.1 9.8
volume (ul) 10 8.2 17 9.5 15 9.3 20 10.5
total (ng) 160 80 115.2 116.8 141 70.5 101.5 103
sample c1 c2 c3 c4 ' d1 d2 d3 d4
concentration (ng/ul) 13 7.2 4.9 5.4 14 7.8 6.6 7.4
volume (ul) 10 9 19 17.5 10 9 15 14
total (ng) 130 65 93.6 95 140 70 100.8 102.2
sample e1 e2 e3 e4 ' f1 f2 f3 f4
concentration (ng/ul) 11 3.1 3.4 4.7 9.5 5.5 2.2 4.6
volume (ul) 7.3 13 17 12.5 2.9 2.5 9 4.4
total (ng) 80.3 40.15 57.8 58.6 27.5 13.8 19.8 20
sample DF1 DF2 DF3 DF4 ' FS1 FS2 FS3 FS4
concentration (ng/ul) 17.7 10.1 6.2 11.7 15.3 4.1 5.4 5.2
volume (ul) 9.2 8.1 19 10.2 8.6 16 18 18.5
total (ng) 163.6 81.8 117.8 119.4 131.8 65.9 95 111.7
perform E-gel size selection after pooling all the samples together (8 total):
assume 70% recovery rate, the total amount of DNA in each sample set is:
PGP1_070809: 25ul (330.4ng)
PGP2_070809: 30ul (291ng)
PGP3_070809: 32ul (269ng)
NA12878_070809: 26ul (289ng)
PGP5_070809: 31ul (166ng)
PGP7_070809: 17ul (65ng)
DF6-9-9_070809: 33ul (177ng)
foreskin_070809: 44ul (283ng)
Since PGP7 had very little amount of DNA, it was not send out for shearing. And I will need to repeat the capture on sample f3.
Sent out the following tubes for Covaris shearing to Dr. Billy Li (Harvard) on 7/8/09
PGP1_070809: 25ul (13ng/ul)
PGP2_070809: 30ul (9.7ng/ul)
PGP3_070809: 32ul (8.4ng/ul)
NA12878_070809: 26ul (11ng/ul)
PGP5_070809: 31ul (5.5ng/ul)
DF6-9-9_070809: 33ul (5.4ng/ul)
foreskin_070809: 44ul (6.4ng/ul)