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Forum: Illumina/Solexa 08-31-2017, 06:08 AM
Replies: 16
Views: 2,795
Posted By gabrieltw
@pzucchel My answer to your question only...

@pzucchel

My answer to your question only applies to our own situation. Depends on what a lab is doing, I think you will get different answers.

For us, we process 200+ samples a week from...
Forum: Illumina/Solexa 08-11-2016, 04:28 AM
Replies: 17
Views: 2,790
Posted By gabrieltw
Quant-iT PicoGreen dsDNA Assay Kit can do the...

Quant-iT PicoGreen dsDNA Assay Kit can do the plate format
Forum: Sanger/Dye Terminator 06-02-2016, 03:26 AM
Replies: 7
Views: 2,325
Posted By gabrieltw
As far as I know, the plate septas for our 3730...

As far as I know, the plate septas for our 3730 have been in the lab for 10 years+. All we do is soak, wash, rinse and they still work fine. Just FYI, we use our 3730 heavily so I think it's safe to...
Forum: Sample Prep / Library Generation 05-12-2016, 02:51 AM
Replies: 4
Views: 588
Posted By gabrieltw
If I remember correctly, different AFA tubes have...

If I remember correctly, different AFA tubes have their DNA input limit. MicroTube is about 10 ug max and miniTube is about 20 ug max.
Forum: Sample Prep / Library Generation 03-30-2016, 09:51 AM
Replies: 15
Views: 2,144
Posted By gabrieltw
I work with both. Since you are using tubes, it's...

I work with both. Since you are using tubes, it's actually very easy to reduce the elution volume. I regularly elute in 10-15 uL using eppendorf tube
Forum: Sample Prep / Library Generation 03-30-2016, 05:24 AM
Replies: 15
Views: 2,144
Posted By gabrieltw
How you do pool your library ? If you use...

How you do pool your library ?

If you use beads, just use less elution buffer to elute your library or just use SpeedVac to increase the concentration ?
Forum: Sample Prep / Library Generation 03-29-2016, 11:14 AM
Replies: 15
Views: 2,144
Posted By gabrieltw
I usually try to keep my NaOH concentration less...

I usually try to keep my NaOH concentration less than 1 mM in loading library. I noticed that illumina is using 0.1 N on miniseq library dilution. I have never tried it with 0.1N, I use 0.2N from...
Forum: Sample Prep / Library Generation 03-29-2016, 09:34 AM
Replies: 15
Views: 2,144
Posted By gabrieltw
How did you load 15pM from 1.1 nM library ?

How did you load 15pM from 1.1 nM library ?
Forum: General 02-27-2016, 03:08 AM
Replies: 12
Views: 1,242
Posted By gabrieltw
That has nothing to do with user data. Whatever...

That has nothing to do with user data. Whatever happens between the sequencing center and the machines owners has nothing to do with the 3rd party data.

I am assuming this is related to your...
Forum: General 02-27-2016, 02:35 AM
Replies: 12
Views: 1,242
Posted By gabrieltw
Even a big company like 23andMe needs user...

Even a big company like 23andMe needs user consent to share data. All the sequencing are done on 23andMe's machine but they cannot use those data freely with consent of the users.

Same with all...
Forum: General 02-27-2016, 01:57 AM
Replies: 12
Views: 1,242
Posted By gabrieltw
I think the data belongs to the person who owns...

I think the data belongs to the person who owns the library that was ran on the machine.

Not the machine owner, not the person who operate the machine.

It's like musician owns their music, not...
Forum: Illumina/Solexa 02-22-2016, 11:59 AM
Replies: 49
Views: 8,005
Posted By gabrieltw
Basespace account is not tied to any particular...

Basespace account is not tied to any particular MiSeq as far as I know.

If you are the owner of the basespace account, you should have no issue accessing data that is stored on basespace even if...
Forum: Illumina/Solexa 01-19-2016, 04:40 AM
Replies: 2
Views: 556
Posted By gabrieltw
Even if the run stop with error, you should be...

Even if the run stop with error, you should be able to generate fastq file.

See
...
Forum: Core Facilities 09-30-2015, 09:39 AM
Replies: 1
Views: 1,564
Posted By gabrieltw
We use Perkin Elmer Zephyr compact Liquid...

We use Perkin Elmer Zephyr compact Liquid handler.

Being able to handle 96 wells format at the same time is one of the reason we picked Zephyr. So far it has work well and we can make illumina...
Forum: Sample Prep / Library Generation 09-18-2014, 09:39 AM
Replies: 7
Views: 792
Posted By gabrieltw
How many BACs are you planning on sequencing for...

How many BACs are you planning on sequencing for each run ? We did this on MiSeq and we usually pool 192 BACs in one run. We have 384 barcodes so we rotate them for each run
Forum: Sample Prep / Library Generation 09-18-2014, 09:17 AM
Replies: 7
Views: 792
Posted By gabrieltw
Instead of combination pooling, we just use...

Instead of combination pooling, we just use custom barcodes to make library for BACs and then pool everything together at the end for sequencing. How large is the BAC library do you plan on...
Forum: Illumina/Solexa 07-24-2014, 01:43 PM
Replies: 49
Views: 8,005
Posted By gabrieltw
Why didn't you jut buy the machines directly from...

Why didn't you jut buy the machines directly from them instead of via the university ?
Forum: Illumina/Solexa 07-23-2014, 04:13 AM
Replies: 49
Views: 8,005
Posted By gabrieltw
I am curious about this too.

I am curious about this too.
Forum: Sample Prep / Library Generation 07-10-2013, 04:18 AM
Replies: 14
Views: 7,547
Posted By gabrieltw
Between 5 ul and 15 ul, you are looking at a very...

Between 5 ul and 15 ul, you are looking at a very small difference of total PEG between each ratio. PEG % is very important.

Increase the beads you are using 10x might give you a better result.
Forum: Sample Prep / Library Generation 05-05-2013, 12:30 PM
Replies: 4
Views: 2,236
Posted By gabrieltw
The RSB is 10 mMTris-HCl pH 8.5. It should be fine

The RSB is 10 mMTris-HCl pH 8.5. It should be fine
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