AlanFung:LabNotes/2015/2015-6-3: Difference between revisions

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* Called IGM to reserve the Covaris Shearing Machine.
* Called IGM to reserve the Covaris Shearing Machine.
* I will shear 400ng of samples in case we need to repeat experiment again.
* I will shear 400ng of samples in case we need to repeat experiment again.
*
{| class="wikitable"
|- style="font-size:12pt" align="center" valign="bottom"
| width="43" height="15" | Sample
| width="108" | Sample conc. (ng/ul)
| width="114" | Volume for 400ng (ul)
| width="114" | H2O (ul)
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_1
| align="center" | 21.7
| align="center" | 18.43
| align="center" | 91.57
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_2
| align="center" | 54
| align="center" | 7.41
| align="center" | 102.59
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_3
| align="center" | 57.3
| align="center" | 6.98
| align="center" | 103.02
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_4
| align="center" | 71.9
| align="center" | 5.56
| align="center" | 104.44
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_5
| align="center" | 39.5
| align="center" | 10.13
| align="center" | 99.87
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_6
| align="center" | 29.4
| align="center" | 13.61
| align="center" | 96.39
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_7
| align="center" | 33.7
| align="center" | 11.87
| align="center" | 98.13
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_8
| align="center" | 38.3
| align="center" | 10.44
| align="center" | 99.56
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_9
| align="center" | 32.1
| align="center" | 12.46
| align="center" | 97.54
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_10
| align="center" | 24
| align="center" | 16.67
| align="center" | 93.33
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_11
| align="center" | 40.3
| align="center" | 9.93
| align="center" | 100.07
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_12
| align="center" | 46.3
| align="center" | 8.64
| align="center" | 101.36
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_13
| align="center" | 27.8
| align="center" | 14.39
| align="center" | 95.61
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_14
| align="center" | 29.5
| align="center" | 13.56
| align="center" | 96.44
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_15
| align="center" | 35.2
| align="center" | 11.36
| align="center" | 98.64
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | BR_16
| align="center" | 39
| align="center" | 10.26
| align="center" | 99.74
 
|}

Revision as of 00:55, 9 June 2015

Background

  • Noi made a batch of WGBS libraries on the whole blood DNA from Dr. Rana’s lab.
  • Dr. Rana has obtained some sequencing fund, and would like to get them sequenced.
  • If the libraries are good, can you tell Alan where to locate those libraries, so that we can send them to BioGem?
  • Noi's wiki [[1]]
  • Dinh found the gDNA samples from Dr. Rana in Noi's box.
  • Noi's wiki page shows that the library preparation failed and didn't have time to repeat experiment [[2]]
  • From the labels, Noi got about 1 ug of the samples and only used 200 ng, we should have 800ng for library prep.
  • I will repeat the library prep follow the exact protocol that you did with the tumor WGBS libraries?
  • Noi confirmed that the experiment failed for the first round of experiment and she did try a second time and still the result was not very good
  • She got very faint smear or barely see a smear in many samples by amplifying about 16-18 cycles, which is very unlikely for DNA input ~100ng
  • Noi doesn't know why this is the case but I will give a a try.

Covaris gDNA shearing (2015-06-09)

  • Called IGM to reserve the Covaris Shearing Machine.
  • I will shear 400ng of samples in case we need to repeat experiment again.
Sample Sample conc. (ng/ul) Volume for 400ng (ul) H2O (ul)
BR_1 21.7 18.43 91.57
BR_2 54 7.41 102.59
BR_3 57.3 6.98 103.02
BR_4 71.9 5.56 104.44
BR_5 39.5 10.13 99.87
BR_6 29.4 13.61 96.39
BR_7 33.7 11.87 98.13
BR_8 38.3 10.44 99.56
BR_9 32.1 12.46 97.54
BR_10 24 16.67 93.33
BR_11 40.3 9.93 100.07
BR_12 46.3 8.64 101.36
BR_13 27.8 14.39 95.61
BR_14 29.5 13.56 96.44
BR_15 35.2 11.36 98.64
BR_16 39 10.26 99.74