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Old 06-29-2010, 11:39 AM   #1
epibio
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Default New rRNA removal kit for RNA-Seq

EPICENTRE’s new Ribo-Zero™ rRNA Removal Kit (Human/Mouse/Rat) removes >99% of the 28S, 18S, and 5.8S and >95% of the 5S rRNA from both intact and partially degraded human, mouse, and rat total RNA preparations. RNA-Seq of libraries prepared from partially degraded human reference RNA treated with the Ribo-Zero Kit showed that only 2% of the reads mapped to rRNA sequences, as compared to 63% with a competitive rRNA reduction kit.

For more information, see the product page, or PM me if you're interested in evaluating the kit with other eukaryotic species.

Thanks!
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Old 06-30-2010, 05:44 AM   #2
krobison
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Have you tried this kit with much smaller input amounts of RNA? Could you use <=100ng of input RNA like the DSN protocol which Illumina has?
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Old 06-30-2010, 07:49 AM   #3
epibio
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Although the current kit is not configured specifically for low input, we do have customers who have scaled the protocol for use with ~50 ng total RNA. You would need additional spin filters since you're processing more samples than the kit was designed for, but it will work.
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Old 07-08-2010, 12:43 AM   #4
nanos
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Is it possible to use this kit for Drosophila melanogaster mRNA purification?
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Old 07-08-2010, 07:16 AM   #5
epibio
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Although we have not tried it with Drosophila, it should work. If you're interested in trying it, please PM me and I can arrange for an evaluation kit.
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Old 09-23-2010, 07:03 PM   #6
SeqMonster
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Is there a protocol that can couple bacterial and human rRNA removal from a total RNA prep?
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Old 09-24-2010, 07:48 AM   #7
epibio
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You could run one round of the Human/Mouse/Rat rRNA removal procedure, followed by one round of the bacterial (Gram-negative) procedure. However, the results will be affected by the relative amounts of bacterial and human RNA in your samples.
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Old 12-15-2010, 03:06 PM   #8
SeqMonster
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This product looks good. I would like to give it a try. What is the method based on?
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Old 12-16-2010, 08:23 AM   #9
epibio
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It's a proprietary hybridization-based method that is designed to remove rRNA from both intact and fragmented (partially degraded) total RNA.
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Old 12-20-2010, 02:31 PM   #10
SeqMonster
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Great. I am interested in evaluating the kit with my sample. Is there any way to mix the Ribozero for human and bacteria (both gram positive and gram negative) in one step to minimize mRNA degradation due to handling?
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Old 12-21-2010, 09:40 AM   #11
epibio
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We haven't tested a mix, but should be theoretically possible if you know the relative amounts of human vs. bacterial RNA in your samples.
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Old 01-06-2011, 07:37 AM   #12
jiaoyuchen
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I'm very interested in the kit. We have tried RiboMinus from invitrogen before. The removal effect was not satisfying. Can I have an evaluation kit for human samples? Thank you!
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Old 01-06-2011, 11:18 AM   #13
epibio
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Please contact me using the link in my profile and I'd be happy to set you up with the evaluation program. Thank you.
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Old 01-13-2011, 09:55 AM   #14
valfdz
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Hello.

Can I use this kit whit Cyanobacteria?? Someone probe it??
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Old 01-14-2011, 11:50 AM   #15
epibio
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We have not tested the kit with Cyanobacteria.
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Old 04-28-2011, 03:47 PM   #16
rdesprat
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What is the level of degradation of RNA induced by the kit?Many people are telling me that they are getting degraded rna at the end of the ribozero kit...do you have a way to check that?
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Old 04-28-2011, 04:47 PM   #17
SeqMonster
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You can use Agilent Bioanalyzer RNA chip to check your RNA integrity.
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Old 04-29-2011, 07:01 AM   #18
NextGenSeq
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Since the first step in making an RNA-Seq library is fragmenting the RNA I don't see why degradation would be a problem.
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Old 04-29-2011, 12:01 PM   #19
epibio
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We haven't seen degradation when testing for common transcripts on Northerns. You do retain the small-RNA fraction after purification if you use the recommended Zymo columns; perhaps this is being confused for degradation products.
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Old 05-24-2011, 01:03 PM   #20
SysBioNaMA
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Hello,

I am involve in mixed microbial community research and i plan to realise a deep sequencing mRNA on total bacterial popuation. You propose two different Ribo-Zero rRNA removal kit for bacteria, one specific for Gram positive bactria and an other one specific to Gram negative bacteria. Nevertheless I interessted by rRNA removal on total RNA present. Could you tell me which kit match best with my project?

Tanks
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