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Search: Posts Made By: luc
Forum: General 02-23-2021, 02:21 PM
Replies: 2
Views: 166
Posted By luc
Hi, multiple companies offer spin columns and...

Hi, multiple companies offer spin columns and spin plates.

E.g.
http://www.epochlifescience.com/Product/SpinColumn/minispin.aspx
https://bpi-tech.com/96-well-plates/

I have not used these...
Forum: Oxford Nanopore 11-30-2020, 09:45 AM
Replies: 1
Views: 1,167
Posted By luc
No remodeling needed. All Nextera libraries...

No remodeling needed.
All Nextera libraries are PCR amplified to be sequenceable. After the PCR amplification they are wonderfully double-stranded throughout and should be blunt-ended (if a...
Forum: Sample Prep / Library Generation 10-01-2020, 11:09 AM
Replies: 3
Views: 1,182
Posted By luc
You might want to have a look at this FAQ: ...

You might want to have a look at this FAQ:
https://dnatech.genomecenter.ucdavis.edu/faqs/my-pcr-free-libraries-do-not-look-as-expected-on-the-bioanalyzer-how-should-i-qc-pcr-free-libraries/
Forum: Sample Prep / Library Generation 10-01-2020, 10:57 AM
Replies: 5
Views: 1,556
Posted By luc
Depends on the dye used and the amount of...

Depends on the dye used and the amount of primers. Ethidiumbrmide is ten times less sensitive for ssDNA compared to dsDNA. The sampe seems to be true for the Bioanalyzer, but such an instrument is...
Forum: Sample Prep / Library Generation 09-26-2020, 07:39 AM
Replies: 5
Views: 1,556
Posted By luc
You could run aliquots of the reaction (before...

You could run aliquots of the reaction (before and after bead cleanups) on an agarose gel to see what is going on.
If the ligation does not work porperly, perhaps your samples have some chemical...
Forum: Sample Prep / Library Generation 09-18-2020, 12:26 AM
Replies: 5
Views: 1,755
Posted By luc
Add Qiagen UPX to the list.

Add Qiagen UPX to the list.
Forum: Sample Prep / Library Generation 09-14-2020, 11:23 PM
Replies: 5
Views: 1,755
Posted By luc
What is your goal? Gene-level studies or...

What is your goal? Gene-level studies or transcript level?
Forum: General 08-05-2020, 02:30 PM
Replies: 1
Views: 2,066
Posted By luc
One more important alternative is the Perkin...

One more important alternative is the Perkin Elmer Labchip GX Touch.
They all work and differ in the resolution, throughput, reagent costs and setup effort.
Forum: Illumina/Solexa 08-02-2020, 06:18 PM
Replies: 3
Views: 1,236
Posted By luc
I beleive there is no reason to expect the run to...

I beleive there is no reason to expect the run to fail now. The data should be usable as indicated by the qualityscores.
Forum: Illumina/Solexa 08-01-2020, 05:59 PM
Replies: 3
Views: 1,236
Posted By luc
The run is still ongoing? More information...

The run is still ongoing?
More information would be rquired.
Forum: Sample Prep / Library Generation 07-25-2020, 08:17 PM
Replies: 1
Views: 1,623
Posted By luc
Sorry, the attachments do not open for me.

Sorry, the attachments do not open for me.
Forum: Oxford Nanopore 07-24-2020, 12:53 PM
Replies: 7
Views: 3,351
Posted By luc
In our experience the ligation and associated...

In our experience the ligation and associated reagents is the most sensitive part of library preps. I would expect other reagents to last longer past the expiration date, but I won't make any...
Forum: Illumina/Solexa 07-23-2020, 06:15 PM
Replies: 1
Views: 1,437
Posted By luc
Yes, you definitely want to QC your library for...

Yes, you definitely want to QC your library for the fragment lengths before sequencing using a Bioanalyzer or equivalent devices.
Forum: Introductions 07-23-2020, 06:09 PM
Replies: 1
Views: 1,431
Posted By luc
Cogito ergo seq. Welcome

Cogito ergo seq.

Welcome
Forum: Oxford Nanopore 07-22-2020, 02:26 PM
Replies: 7
Views: 3,351
Posted By luc
Three months should not make a meaningful...

Three months should not make a meaningful difference with these reagents - if they were stored properly.
Forum: Bioinformatics 06-18-2020, 09:18 PM
Replies: 1
Views: 1,380
Posted By luc
For a plant or an animal?

For a plant or an animal?
Forum: Sample Prep / Library Generation 06-05-2020, 06:20 PM
Replies: 1
Views: 1,969
Posted By luc
I have never seen any problems with DNA samples...

I have never seen any problems with DNA samples in EBT or EB buffer.
This tiny amount of detergent does not seem to cause problems.
I agree with avoiding EDTA buffers;at least at 1 mM...
Forum: Illumina/Solexa 05-13-2020, 01:27 PM
Replies: 2
Views: 2,027
Posted By luc
Could you let us know what specific problems you...

Could you let us know what specific problems you see with the data (and the DNA samples?)?
Forum: Introductions 04-28-2020, 01:55 PM
Replies: 5
Views: 2,370
Posted By luc
Also: bioinformatics.ucdavis.edu

Also: bioinformatics.ucdavis.edu
Forum: Illumina/Solexa 04-24-2020, 09:26 PM
Replies: 2
Views: 1,943
Posted By luc
Who is advertising this? Hard to tell what it...

Who is advertising this?
Hard to tell what it means - there are soo many different library prep chemistry options.
Forum: Sample Prep / Library Generation 04-16-2020, 04:20 PM
Replies: 6
Views: 1,932
Posted By luc
A secret tip:...

A secret tip:...
Forum: Bioinformatics 04-14-2020, 10:57 PM
Replies: 1
Views: 797
Posted By luc
Very likely the ONT data are not suitable for the...

Very likely the ONT data are not suitable for the kmer analysis. The read error rate is likely too high. Every 27 nt stretch can be expected to contain errors?

This will work with Illumina or HiFi...
Forum: Sample Prep / Library Generation 03-31-2020, 07:50 PM
Replies: 4
Views: 2,372
Posted By luc
Thanks!!! This is a neat idea.

Thanks!!!
This is a neat idea.
Forum: Illumina/Solexa 03-05-2020, 04:40 PM
Replies: 2
Views: 1,408
Posted By luc
This is expected. You are sequencing through the...

This is expected. You are sequencing through the poly-A tail. You can ignore this part of the data, and sequence only ~30 (?) cycles for the forward read next time.
Forum: Sample Prep / Library Generation 02-06-2020, 09:22 PM
Replies: 1
Views: 1,494
Posted By luc
I believe you can use standard barcoded Nextera...

I believe you can use standard barcoded Nextera primers instead. Preferentially UDI dual indexed versions of the Nextera primers.
Simple desalted oligos will be fine indeed.
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