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Search: Posts Made By: SueFoltin
Forum: Illumina/Solexa 09-11-2017, 05:52 AM
Replies: 17
Views: 2,113
Posted By SueFoltin
Yeah, we were quite surprised when I spoke to...

Yeah, we were quite surprised when I spoke to them and discovered this. In the future we might ask them to use all and increase the cycles to 14 or 15. That would explain A LOT of reasons why we...
Forum: Illumina/Solexa 09-08-2017, 10:06 AM
Replies: 17
Views: 2,113
Posted By SueFoltin
jteeee2 - thank you for the primer and Taq...

jteeee2 - thank you for the primer and Taq information. I just spoke with the technicians at the CORE again. It seems that they hold back some of the cDNA with adaptors, so all I need are the...
Forum: Illumina/Solexa 09-08-2017, 10:00 AM
Replies: 17
Views: 2,113
Posted By SueFoltin
Thanks for the heads up. I'll definitely forward...

Thanks for the heads up. I'll definitely forward this information to our sequencing CORE facility.
Forum: Illumina/Solexa 09-06-2017, 12:04 PM
Replies: 17
Views: 2,113
Posted By SueFoltin
I don't think they run controls, unfortunately. ...

I don't think they run controls, unfortunately. We wondered about that too. I think we are going to request the library material be returned to us and we'll proceed with the extra 3-4 cycles of...
Forum: Illumina/Solexa 09-06-2017, 11:31 AM
Replies: 17
Views: 2,113
Posted By SueFoltin
The ng/uL are based on Qubit while the ratios...

The ng/uL are based on Qubit while the ratios were determined with the Nanodrop. I don't think I've really tested to see if there is contaminating DNA as we do perform the DNase I step and perform...
Forum: Illumina/Solexa 09-06-2017, 10:57 AM
Replies: 17
Views: 2,113
Posted By SueFoltin
Thank you for all your suggestions. I am...

Thank you for all your suggestions. I am attaching several files. The "Final RNA run successful" excel sheet was our previous run where all the samples worked using 12 cycles of PCR, no...
Forum: Illumina/Solexa 09-04-2017, 11:05 AM
Replies: 17
Views: 2,113
Posted By SueFoltin
Getting TruSeq to work with RNA samples

So have isolated RNA from FFPE. Originally our isolations were performed using the Qiagen AllPrep kits. Now we are using the RNA/DNA STORM kits from Cell Data Sciences.

We have a CORE that takes...
Forum: Illumina/Solexa 06-27-2017, 04:05 AM
Replies: 4
Views: 760
Posted By SueFoltin
What should be used? I know they are running RIN...

What should be used? I know they are running RIN and DV200. Illumina has provided them with guidelines on how long to fragment on the Covarius based on the DV200. I know there is an enzymatic...
Forum: Illumina/Solexa 06-26-2017, 05:54 PM
Replies: 4
Views: 760
Posted By SueFoltin
Is there an upper limit for RNA input

We have been having issues with our RNA from FFPE when submitting for sequencing. We are using the Illumina kit RS-122-2201, TruSeq Stranded Total RNA RboZroHMN/Mse/Rat with ribo depletion.

Our...
Forum: Illumina/Solexa 06-09-2017, 05:33 AM
Replies: 3
Views: 1,593
Posted By SueFoltin
Lexogen and jteeee2: Thank you so much. I...

Lexogen and jteeee2:
Thank you so much. I really didn't expect anyone to respond as most don't work with FFPE. These are the only tissue source we tend to have issues with and having the...
Forum: Illumina/Solexa 06-08-2017, 05:51 AM
Replies: 3
Views: 1,593
Posted By SueFoltin
RNA from FFPE vs quality for Illumina Seq

We have hundreds of RNA samples isolated from FFPE using the Qiagen AllPrep kit. I should point out that we have adapted the QIagen's protocol to add an additional RPE wash AS WELL AS an additional...
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