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RNA-Seq: RSeQC: Quality Control of RNA-seq experiments. Newsbot! Literature Watch 0 06-30-2012 02:00 AM
RNA-Seq: A pipeline for RNA-seq data processing and quality assessment. Newsbot! Literature Watch 0 01-15-2011 02:50 AM

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Old 06-30-2013, 07:38 AM   #1
lior lobel
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Question Help with determining RNA quality for RNA SEQ

Hi All,

I'm new to RNA-Seq, so I'm not that familier with RNA quality checks for RNA seq. I have 6 total bacterial RNA samples, that I want to carry for rRNA depletion using the RiboZero kit. Before doing that I ran the samples on agarose gel and got a strange result (please see attached). It seems that all the samples have a huge band around 100bp.. what this means? is that degraded RNA? or maybe DNaseI degraded DNA leftovers?
Any help interpreting this gel will be highly appreciated!

Thanks and best,

Lior
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File Type: pdf Agarose gel.pdf (63.8 KB, 36 views)
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Old 07-05-2013, 05:49 AM   #2
HelenaSC
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Hi Lior,

Don't you have the possibility to check your samples with a Bioanalyzer or similar??
I think it would be better...
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Old 07-05-2013, 06:20 AM   #3
lior lobel
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Hi Helena,

Just yesterday did the bioanalyzer analysis. please see attached. This is after rRNA depletion by RiboZero and by mistake the analysis was done with Eukaryotic reference.

The big 100-140 nt peak is tRNAs and sRNAs, right?

Thanks and Good weekend,

Lior
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File Type: pdf Eukaryote Total RNA Pico_2013-07-04_13-42-55.pdf (1.47 MB, 45 views)
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Old 07-05-2013, 06:30 AM   #4
HelenaSC
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Yes, you are right, the peak should be miRNA, tRNA and so on.
Good weekend!
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Old 04-22-2016, 03:14 AM   #5
mRNA123
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This paper has a nice method of assessing RNA quality not based on rRNA. Essentially they look for degradation from the 3' end based on RT-qPCR products from the same RNA using the same forward primer and various reverse primers. Assuming 3'-to-5' decay, a sample with extensive RNA decay will have less of the RT-qPCR products near the 3' end.
http://www.gene-quantification.de/bj...p-bdq-2016.pdf
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rna integrity, rna profiling, rna quality

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