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Forum: RNA Sequencing 02-28-2018, 05:22 AM
Replies: 2
Views: 1,553
Posted By l_zembek
You may be more interested in TopHat fusion for...

You may be more interested in TopHat fusion for this purpose:
https://ccb.jhu.edu/software/tophat/fusion_index.shtml
Forum: RNA Sequencing 02-07-2018, 11:16 AM
Replies: 0
Views: 1,513
Posted By l_zembek
5' RNA-Seq Bias?

What are some possible reasons for 5->3' bias in RNA seq data? Libraries were generated using Illumina's TruSeq Stranded mRNA protocol, with pretty good quality RNA input. If anything, with a polyA...
Forum: Sample Prep / Library Generation 05-23-2013, 03:49 AM
Replies: 2
Views: 1,185
Posted By l_zembek
Thank you very much, that's likely how I'll...

Thank you very much, that's likely how I'll proceed. I was going to use RNase A, but base hydrolysis is likely more cost effective, especially for a lot of samples.
Forum: Sample Prep / Library Generation 05-22-2013, 07:16 AM
Replies: 2
Views: 1,185
Posted By l_zembek
Separation of total nucleic acid?

We are using the Chemagen system (http://www.chemagen.com/fileadmin/downloads/101115_Automation_brochure.pdf) to extract total nucleic acid from blood and stool samples. The process yields a mixture...
Forum: Sample Prep / Library Generation 05-07-2013, 08:29 AM
Replies: 2
Views: 1,840
Posted By l_zembek
Thanks for your comment, "austinso." A 1:5...

Thanks for your comment, "austinso." A 1:5 dilution followed by a 1.8X SPRI cleanup seems to have gotten most samples to a consistency suitable for pico quant. But shearing would've been my next...
Forum: Sample Prep / Library Generation 04-11-2013, 05:58 AM
Replies: 2
Views: 1,840
Posted By l_zembek
Viscous samples?

I have received a large set of extracted DNA samples that are extremely viscous, and am unable to pico or process them in any way. I've tried diluting, heating, shaking, proteinase K, Ampure bead...
Forum: Illumina/Solexa 03-19-2013, 12:05 PM
Replies: 6
Views: 3,715
Posted By l_zembek
Thank you for your comments! I think I'll try...

Thank you for your comments! I think I'll try the PippinPrep, since we have one, and have had good results at isolating bands in that size range.

It does appear that using adapters with...
Forum: Illumina/Solexa 03-19-2013, 07:38 AM
Replies: 6
Views: 3,715
Posted By l_zembek
Small RNA-Seq Kits

I need to prepare some miRNA libraries for Illumina sequencing, and have been looking at what's available. Does anyone have any experience with any of these kits, good or bad?

-TruSeq Small RNA...
Forum: RNA Sequencing 03-19-2013, 07:38 AM
Replies: 0
Views: 1,451
Posted By l_zembek
Small RNA-Seq Kits

I need to prepare some miRNA libraries for Illumina sequencing, and have been looking at what's available. Does anyone have any experience with any of these kits, good or bad?

-TruSeq Small RNA...
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