Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

bioanalyzer results - better than first round? #792

Closed
grace-ac opened this issue Nov 7, 2019 · 8 comments
Closed

bioanalyzer results - better than first round? #792

grace-ac opened this issue Nov 7, 2019 · 8 comments
Assignees
Labels

Comments

@grace-ac
Copy link
Contributor

@grace-ac grace-ac commented Nov 7, 2019

@kubu4 do these seem better than the first round?

Should I continue with the rest of my samples?

I think they look a little better.... ?

First round:

gel

bairdi-firstround-gel

electropherogram

bairdi-firstround-electro

Second round (after confirming that reagents all work, but without ladder (need new ladder aliquots)):

gel

bairdi-gel

electropherogram

bairdi-electropherogram

@grace-ac grace-ac added the question label Nov 7, 2019
@grace-ac grace-ac changed the title bioanalyzer results - no ladder bioanalyzer results - better than first round? Nov 7, 2019
@kubu4

This comment has been minimized.

Copy link
Contributor

@kubu4 kubu4 commented Nov 7, 2019

Samples don't look good and seem to be interfering with the marker. Check samples on NanoDrop.

@grace-ac

This comment has been minimized.

Copy link
Contributor Author

@grace-ac grace-ac commented Nov 7, 2019

Sample ID User ID Date Time ng/ul A260 A280 260/280 260/230 Constant Cursor Pos. Cursor abs. 340 raw
10 Default 11/6/2019 4:47 PM 40.03 1.001 0.486 2.06 0.32 40.00 230 3.117 0.038
169 Default 11/6/2019 4:48 PM 51.50 1.288 0.599 2.15 1.92 40.00 230 0.671 0.020
29 Default 11/6/2019 4:49 PM 49.92 1.248 0.630 1.98 1.33 40.00 230 0.937 0.128
119 Default 11/6/2019 4:50 PM 33.50 0.838 0.486 1.72 0.22 40.00 230 3.826 5.695
119 Default 11/6/2019 4:52 PM 7.22 0.180 0.076 2.38 0.06 40.00 230 3.049 -1.480
177 Default 11/6/2019 4:53 PM 24.73 0.618 0.293 2.11 1.08 40.00 230 0.575 0.196
24 Default 11/6/2019 4:54 PM 26.51 0.663 0.319 2.08 1.13 40.00 230 0.588 0.025
111 Default 11/6/2019 4:55 PM 23.54 0.589 0.296 1.99 0.22 40.00 230 2.637 0.138
124 Default 11/6/2019 4:57 PM 15.28 0.382 0.170 2.24 0.57 40.00 230 0.675 0.016
53 Default 11/6/2019 4:59 PM 20.58 0.514 0.272 1.89 0.10 40.00 230 5.414 0.015
91 Default 11/6/2019 5:00 PM 15.70 0.392 0.201 1.96 0.19 40.00 230 2.022 0.621
81 Default 11/6/2019 5:01 PM 24.68 0.617 0.305 2.02 0.22 40.00 230 2.814 0.021
@grace-ac

This comment has been minimized.

Copy link
Contributor Author

@grace-ac grace-ac commented Nov 7, 2019

I ran 119 twice because it gave this error (also gave same error after I tried again):
nano-119

@grace-ac

This comment has been minimized.

Copy link
Contributor Author

@grace-ac grace-ac commented Nov 7, 2019

I took screenshots of all graphs

@kubu4

This comment has been minimized.

Copy link
Contributor

@kubu4 kubu4 commented Nov 7, 2019

NanoDrop results look perfect (260/280 at ~2.0 for all samples; 260/230 < 2.0 for all samples).

Two suggestions:

  1. Run a chip and use the kit's elution buffer as your "sample". This will see if elution buffer is causing issues with Bioanalyzer (i.e. causing marker to fail).

  2. Run some of the RNA samples I used for most recent round of RNAseq and see how they compare. Choose some from successful libraries and some from unsuccessful libraries.

@grace-ac

This comment has been minimized.

Copy link
Contributor Author

@grace-ac grace-ac commented Nov 7, 2019

New plan:

  1. Run four samples from the above group on Qubit using DNA HS
  2. Use Turbo DNA-free Kit on those samples
  3. Run those samples on Bioanalyzer
  4. Re-run those samples on Qubit using DNA HS
@grace-ac

This comment has been minimized.

Copy link
Contributor Author

@grace-ac grace-ac commented Nov 8, 2019

  1. Done --> results
  2. Done (Did the routine DNase treatment)
  3. Done (screenshots below) ran each of the 4 samples twice (##-a and ##-b)
  4. Done - samples were eluted in ~40-45ul
    (ran dsDNA HS results; ran RNA HS results)

bioanalyzer-4samples

bioanalyzer-gel-4samples

@sr320

This comment has been minimized.

Copy link
Member

@sr320 sr320 commented Nov 13, 2019

will go fwd with seq

@sr320 sr320 closed this Nov 13, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
3 participants
You can’t perform that action at this time.