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Search took 0.00 seconds. Search: Posts Made By: jteeee2
Forum: RNA Sequencing 11-04-2020, 06:44 AM
Replies: 2
Views: 3,786
Posted By jteeee2
Both are fine choices so the decision will likely...

Both are fine choices so the decision will likely come down to what sort of transcripts you are interested in looking at. The TruSeq RNA Exome kit is going to give you significantly higher coverage...
Forum: Sample Prep / Library Generation 05-15-2020, 11:22 AM
Replies: 4
Views: 2,064
Posted By jteeee2
Hi Sofia- Could you provide a bit more info on...

Hi Sofia- Could you provide a bit more info on the specific library prep method you used? The first couple of traces look as though they represent a pooled amplicon-based approach. 3 dominant peaks...
Forum: Sample Prep / Library Generation 04-17-2020, 10:38 AM
Replies: 6
Views: 1,938
Posted By jteeee2
There's also this paper that came out a few days...

There's also this paper that came out a few days ago which suggests you don't need to deplete globin at all if you're starting with Paxgene blood. ...
Forum: Illumina/Solexa 04-17-2020, 06:35 AM
Replies: 2
Views: 2,771
Posted By jteeee2
Could try purchasing some new Sodium Hydroxide...

Could try purchasing some new Sodium Hydroxide and Tris for denaturing libraries. If your NaOH is over a year old and has been opened a lot, I'd recommend purchasing a new bottle. The lenses on the...
Forum: Sample Prep / Library Generation 04-17-2020, 06:29 AM
Replies: 6
Views: 1,938
Posted By jteeee2
Agree with @nucacidhunter. We were initially...

Agree with @nucacidhunter. We were initially excited about the new Qiagen product but have also seen some odd performance issues...particularly when including globin-reduction probes. The Illumina...
Forum: Sample Prep / Library Generation 12-12-2017, 10:55 AM
Replies: 10
Views: 2,816
Posted By jteeee2
That material will be fine for a total RNA Seq...

That material will be fine for a total RNA Seq approach. I wouldn't get concerned unless that value is above 10%. Also agree with pmiguel that the Qubit value can be misleading.
Forum: Illumina/Solexa 10-19-2017, 07:50 AM
Replies: 17
Views: 2,627
Posted By jteeee2
Glad to hear things are improving. Best of luck...

Glad to hear things are improving. Best of luck getting those last 23 samples made into libraries.
Forum: RNA Sequencing 09-21-2017, 06:58 AM
Replies: 15
Views: 6,138
Posted By jteeee2
Take a look at Kapa's RNA Seq documentation...

Take a look at Kapa's RNA Seq documentation (https://www.kapabiosystems.com/product-applications/products/next-generation-sequencing-2/rna-library-preparation-2/kapa-stranded-mrna-seq-kits/). They...
Forum: Illumina/Solexa 09-11-2017, 06:51 AM
Replies: 17
Views: 2,627
Posted By jteeee2
For FFPE samples, none of the adaptor-ligated...

For FFPE samples, none of the adaptor-ligated cDNA should be "reserved." All of it should move into the final PCR step. That's my opinion, and I'd be interested to hear what others thought. The P5...
Forum: Illumina/Solexa 09-06-2017, 01:46 PM
Replies: 17
Views: 2,627
Posted By jteeee2
I hope it works out for you. Regardless of...

I hope it works out for you. Regardless of outcome, I'd consider a using a different NGS provider :). Batch controls are incredibly important and often the only way to troubleshoot sample...
Forum: Illumina/Solexa 09-06-2017, 12:50 PM
Replies: 17
Views: 2,627
Posted By jteeee2
Also, did the core run any other samples...

Also, did the core run any other samples alongside yours? Did they include a batch control to verify the reagents were good? The fact that all of your samples performed so poorly makes me wonder if...
Forum: Illumina/Solexa 09-06-2017, 12:39 PM
Replies: 17
Views: 2,627
Posted By jteeee2
Glad to hear these were Qubit measurements. I...

Glad to hear these were Qubit measurements. I was initially concerned that they were Nanodrop readings and you were actually putting far less RNA into the library prep than you thought.

A quick...
Forum: Illumina/Solexa 09-06-2017, 12:26 PM
Replies: 17
Views: 2,627
Posted By jteeee2
That sounds like something Illumina would say. ...

That sounds like something Illumina would say. However, they do market these kits as being appropriate for FFPE material.

In the spreadsheets you attached, are those RNA concentrations nanodrop...
Forum: Illumina/Solexa 09-05-2017, 06:48 AM
Replies: 17
Views: 2,627
Posted By jteeee2
Generating RNA-Seq libraries from FFPE RNA can be...

Generating RNA-Seq libraries from FFPE RNA can be quite frustrating, so I definitely understand where you are coming from.

We haven't been very pleased with the RNA we get out of the Qiagen...
Forum: Sample Prep / Library Generation 08-24-2017, 12:44 PM
Replies: 2
Views: 3,555
Posted By jteeee2
You should be able to manually adjust the fast...

You should be able to manually adjust the fast region signal allowance under the advanced settings and this will clear the error, allowing for a RIN to be called.
Forum: Sample Prep / Library Generation 08-08-2017, 09:37 AM
Replies: 2
Views: 1,799
Posted By jteeee2
If you're really interested DNase treating, we...

If you're really interested DNase treating, we have had good success incorporating this product into the front end of several RNA Seq protocols (including SmartSeq). ...
Forum: Illumina/Solexa 06-08-2017, 02:37 PM
Replies: 3
Views: 2,498
Posted By jteeee2
For column cleanup of your already extracted RNA,...

For column cleanup of your already extracted RNA, I'd recommend the Zymo RNA Clean and Concentrator-5 workflow. Cheap, easy to use, and allows a smaller elution volume than compared to others (i.e....
Forum: Sample Prep / Library Generation 04-18-2017, 07:17 AM
Replies: 15
Views: 3,292
Posted By jteeee2
I agree with nucacidhunter about using the Pico...

I agree with nucacidhunter about using the Pico RNA assay on the Bioanalyzer. It would be interesting to see what this material looks like on the more sensitive assay.

Has this material been...
Forum: Sample Prep / Library Generation 04-17-2017, 03:26 PM
Replies: 15
Views: 3,292
Posted By jteeee2
Standard poly-A capture RNA-Seq protocols can go...

Standard poly-A capture RNA-Seq protocols can go down to about 100 ng of Total RNA starting material these days. Kapa (I don't work for Kapa, but I do like their NGS kits) sells a mRNA HyperPrep kit...
Forum: Illumina/Solexa 03-29-2017, 12:12 PM
Replies: 9
Views: 2,859
Posted By jteeee2
We haven't dealt with this specific situation...

We haven't dealt with this specific situation before, but with that length of identical sequence I would probably aim a little higher with the PhiX for the first attempt (20-30%). Would be...
Forum: Illumina/Solexa 03-29-2017, 08:33 AM
Replies: 9
Views: 2,859
Posted By jteeee2
What kind of libraries are they? Are you...

What kind of libraries are they? Are you expecting diversity to be low throughout the entire read length or just in specific parts?

We have had success with certain types of low diversity...
Forum: Sample Prep / Library Generation 01-24-2017, 07:10 AM
Replies: 6
Views: 2,925
Posted By jteeee2
I think you'll find it to be a pretty solid...

I think you'll find it to be a pretty solid workflow. You should be right around 90% exonic alignment rates with fresh frozen tissue. With FFPE material, we're in the 80-90% range. Best of luck!
Forum: Sample Prep / Library Generation 01-24-2017, 06:51 AM
Replies: 6
Views: 2,925
Posted By jteeee2
Unfortunately, I don't have any head to head...

Unfortunately, I don't have any head to head comparison data to share. The snoRNAs are actually targeted by probes within the RNA Access oligo pool, so in many cases there is nothing you can do do...
Forum: Sample Prep / Library Generation 11-14-2016, 07:14 AM
Replies: 6
Views: 2,925
Posted By jteeee2
We have seen several different snoRNA's soak up...

We have seen several different snoRNA's soak up reads in our analysis. We have been seeing the data improve recently by pre-heating the wash buffer during the second wash following captures. I...
Forum: Illumina/Solexa 09-30-2016, 08:28 AM
Replies: 19
Views: 8,973
Posted By jteeee2
We have both an Eppendorf 5075 TMX and a Perkin...

We have both an Eppendorf 5075 TMX and a Perkin Elmer Sciclone. In terms of NGS capability, the Sciclone is far superior to the Eppendorf 5075. As thermophile mentioned, the real headache is fine...
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