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Forum: Sample Prep / Library Generation 03-31-2018, 12:18 PM
Replies: 5
Views: 2,284
Posted By achamess
Thanks! How about not at all? I suppose there...

Thanks!
How about not at all? I suppose there is no way to know but try. But I'm actually trying to recover this fragment untouched by Tn5. That might not be possible. I may need to recover it...
Forum: Sample Prep / Library Generation 03-31-2018, 08:24 AM
Replies: 5
Views: 2,284
Posted By achamess
Would Tn5 (Nextera) work on a ~100 bp fragment?

I'm using Nextera to tagment full length cDNA from a heterogeneous mixture. Within this mix, there should also be a small dsDNA fragment that is 113 bp long. I do not want the Tn5 to do anything to...
Forum: Bioinformatics 02-18-2017, 08:07 AM
Replies: 1
Views: 2,128
Posted By achamess
How to use HTSeq to count RNA-Seq overlap w/ whole genes (intron+exon) vs. exon only

So I recently performed RNA-seq using the SmartSeq2 on RNA from neuronal nuclei.


My sample was a pool of sorted neuronal nuclei from mouse. Uing STAR to align, I found that about 20% is exonic,...
Forum: RNA Sequencing 02-18-2017, 07:49 AM
Replies: 0
Views: 1,499
Posted By achamess
Interpretation of Gene Body Distribution from nuclear RNA-Seq

Hi all,

So I just did an experiment using isolated RNA from neuronal nuclei. I used Smart-Seq2 to amplify from ~100 pg of input. I got plenty of cDNA that looked good on the Tapestation (single...
Forum: Sample Prep / Library Generation 04-06-2016, 09:22 AM
Replies: 282
Views: 141,295
Posted By achamess
Hi. Thanks so much for all of the info you...

Hi. Thanks so much for all of the info you provide and for developing Smart-seq2.

I used Smart-seq2 the other day for amplifying mRNA from single neuronal nuclei, as well as bulk (100 nuclei)....
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