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With the discontinuation of the Ribozero Bacteria kit Illumina left the whole field of bacterial transcriptomics out in the rain. People in the field, what alternatives do you use now?
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I had a meeting with our Qiagen rep recently who indicated that they may be working on a bacterial rRNA removal kit.
Definitely hoping to find a suitable alternative! -
Vazyme.bio techComment
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Just found that NuGen has a metatranscriptome kit based on their AnyDeplete Technology. Needs to be tested how good/bad the capture efficiency is.Comment
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We just started making riboPOOLs for affordable, custom depletion of ribosomal RNA
Contact us to make a custom riboPOOL to suit your needs - info (at) sitools.deLast edited by siTOOLs; 01-18-2019, 08:34 AM.Comment
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It was recommended that we use Ribominus or Microbexpress as an alternative, but I am having no success with either kit. I sequenced some samples that passed Bioanalyzer qc (no visible residual rRNA) but in both cases anywhere from 70-90% rRNA mapped and very low feature coverage. Has anyone had success with these products or implemented a solid alternative to Ribo-Zero?Comment
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Our group has obtained similar results with the RiboMinus kit. rRNA mapping at ~80%. Alternatives are still needed.Comment
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Just to be sure do you mean 70-90% of final reads are still rRNA? @MU_Core and @evan_seq24?Comment
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Yes, final reads which are rRNA.Comment
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Any update on this?
Several sequencing centers have discouraged MICROBExpress.
I'm interested in the riboPOOL kit (siTOOLs), but they don't reply.
Has anyone experience with this kit? Especially a combination riboPOOL foor soils/sediments (targeting prokaryotes and eukaryotes (plants/chloroplasts, protists, fungi, ...)?
thanks!Comment
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riboPOOLs by siTOOLs
Hi Furor, sorry if you haven't been able to get a reply. If you contact us through our website you should be contacted within 1-2 days. You can also obtain riboPOOLs through our US distributor, Galen Lab Supplies: https://galenmolecular.com/genetic-tools/ribopools/Comment
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According to Illumina (https://www.illumina.com/products/se...ion-guide.html) they have a new product pending for bacteria and plant leaf tissues. They state to contact Tech SupportOriginally posted by furor View PostComment
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Has anyone tried this kit from ZYMO? Usually ZYMO stuff is pretty good...
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Interesting...micrboEXPRESS looks to be an Ambion Kit (originally). But Ambion basically got destroyed when Thermo Fisher bought it...Originally posted by furor View PostComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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