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Forum: RNA Sequencing 04-12-2017, 09:30 AM
Replies: 7
Views: 2,036
Posted By JDSwenson
AAHHH!! I KNOW! I just read the paper yesterday...

AAHHH!! I KNOW! I just read the paper yesterday after I replied to this thread. The run finished 2 weeks ago, so there's no going back. So far, I can't think of a way to mitigate the issue. It would...
Forum: RNA Sequencing 04-11-2017, 03:01 PM
Replies: 7
Views: 2,036
Posted By JDSwenson
Many thanks for the replies and sorry it took me...

Many thanks for the replies and sorry it took me awhile to respond!

After consulting with a bioinformatician and the sequencing core director, we decided to sequence the samples in one lane. The...
Forum: RNA Sequencing 03-10-2017, 06:00 PM
Replies: 7
Views: 2,036
Posted By JDSwenson
RNA-Seq libraries ok for DGE analysis?

Hello all,

I have spent the last several months constructing 48 libraries for RNA sequencing from developing stingray tissue, which I am hoping to sequence on a HiSeq 4000 with 100 bp PE reads.
...
Forum: RNA Sequencing 02-01-2017, 04:03 PM
Replies: 3
Views: 2,871
Posted By JDSwenson
Awesome. Thanks a million, nucacidhunter. I...

Awesome. Thanks a million, nucacidhunter. I really appreciate the link and the explanation. I am the first on my campus to prepare libraries for RNA-Sequencing, so when I run into a problem, it's...
Forum: RNA Sequencing 01-29-2017, 10:42 AM
Replies: 3
Views: 2,871
Posted By JDSwenson
BioAnalyzer RIN/rRNA ratio disparity

Hi all,

I am preparing a few dozen libraries for RNA-sequencing. They all come from stingray embryos in early development. To my knowledge, nobody has extracted RNA from any species within the...
Forum: RNA Sequencing 10-21-2016, 12:52 PM
Replies: 4
Views: 1,733
Posted By JDSwenson
Thank-you for the replies! I've called...

Thank-you for the replies!

I've called tech support and I ran a time series, fragmenting at 5, 7, 10, and 12 minutes. Then I did a cleanup with 2.2x AmPure beads following the RNAClean XP...
Forum: RNA Sequencing 10-17-2016, 08:33 PM
Replies: 4
Views: 1,733
Posted By JDSwenson
Stingray mRNA Fragmentation NEBNext

Hi all,

I am using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina following mRNA isolation using dT beads.

I've been having some trouble with my mRNA fragmentation time. In...
Forum: Sample Prep / Library Generation 04-20-2016, 05:14 PM
Replies: 1
Views: 1,258
Posted By JDSwenson
Size Selection after fragmentation

Hey there,

This is my first post here - thanks for reading it!

I'm rather lost. I'm prepping some samples for RNA-Seq, but in all four of my samples, I lose ~80-90% of my product at the mRNA...
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