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 |