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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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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