Ribozero Bacteria discontinued - alternatives?

Genetic Librarian · 12-03-2018, 01:11 AM

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?

ikripp · 12-04-2018, 07:23 PM

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!

yeyue · 12-04-2018, 11:31 PM

Vazyme.bio tech

Genetic Librarian · 12-06-2018, 06:36 AM

Just found that NuGen has a metatranscriptome kit based on their AnyDeplete Technology. Needs to be tested how good/bad the capture efficiency is.

siTOOLs · 01-18-2019, 08:31 AM

We just started making riboPOOLs for affordable, custom depletion of ribosomal RNA
https://www.sitoolsbiotech.com/ribopools.php

Contact us to make a custom riboPOOL to suit your needs - info (at) sitools.de

evan_seq24 · 01-30-2019, 03:27 PM

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?

MU Core · 01-31-2019, 08:21 AM

Our group has obtained similar results with the RiboMinus kit. rRNA mapping at ~80%. Alternatives are still needed.

GenoMax · 02-01-2019, 04:00 AM

Just to be sure do you mean 70-90% of final reads are still rRNA? @MU_Core and @evan_seq24?

MU Core · 02-01-2019, 05:50 AM

Yes, final reads which are rRNA.

furor · 09-17-2019, 01:04 AM

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!

siTOOLs · 09-17-2019, 02:17 AM

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/

kmcarr · 09-18-2019, 05:56 AM

Quote:

Originally Posted by furor

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!

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 Support

cement_head · 11-11-2019, 06:13 PM

Has anyone tried this kit from ZYMO? Usually ZYMO stuff is pretty good...

https://www.zymoresearch.com/product...ersal-cdna-kit

cement_head · 11-11-2019, 07:26 PM

Quote:

Originally Posted by furor

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!

Interesting...micrboEXPRESS looks to be an Ambion Kit (originally). But Ambion basically got destroyed when Thermo Fisher bought it...

cement_head · 11-12-2019, 04:17 AM

Ha! Talk of the Devil!

New kit by Qiagen...

http://cloud.go.qiagen.com/e/es?s=87...d=6008&elqat=1

GenoMax · 11-12-2019, 04:59 AM

Illumina is going to re-introduce ribozero equivalent kits in 2020.

MU Core · 11-12-2019, 06:45 AM

For those seeking a bacterial rRNA depletion kit, NEB has just released a kit that works very well in our hands.

https://www.neb.com/products/e7850-n...%20Information

jjlin · 02-05-2020, 12:40 PM

Quote:

Originally Posted by cement_head

Has anyone tried this kit from ZYMO? Usually ZYMO stuff is pretty good...

https://www.zymoresearch.com/product...ersal-cdna-kit

DISCLAIMER: I work for Zymo

We have options for people who are interested in doing probe-free depletion. Contact tech@zymoresearch.com and tell them you'd like to try the RiboFree Total RNA Library Kit. We were offering trial sizes and free samples a few months ago.

luc · 02-05-2020, 07:00 PM

According to rumors, RiboZero will make a comeback. Not exactly the same products though; it will use a new chemistry.

GenoMax · 02-06-2020, 05:12 AM

Illumina did release a new version of RiboZero+ yesterday: https://www.illumina.com/products/by...depletion.html

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12-03-2018, 01:11 AM	#1
Genetic Librarian Member Location: Europe Join Date: May 2017 Posts: 31	Ribozero Bacteria discontinued - alternatives? 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?

01-18-2019, 08:31 AM	#5
siTOOLs Junior Member Location: Germany Join Date: Jan 2019 Posts: 2	We just started making riboPOOLs for affordable, custom depletion of ribosomal RNA https://www.sitoolsbiotech.com/ribopools.php Contact us to make a custom riboPOOL to suit your needs - info (at) sitools.de Last edited by siTOOLs; 01-18-2019 at 08:34 AM.

09-17-2019, 02:17 AM	#11
siTOOLs Junior Member Location: Germany Join Date: Jan 2019 Posts: 2	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/

12-04-2018, 07:23 PM	#2
ikripp Member Location: QLD, Aus Join Date: Jan 2018 Posts: 19	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!

12-04-2018, 11:31 PM	#3
yeyue Junior Member Location: china Join Date: Feb 2018 Posts: 2	Vazyme.bio tech

12-06-2018, 06:36 AM	#4
Genetic Librarian Member Location: Europe Join Date: May 2017 Posts: 31	Just found that NuGen has a metatranscriptome kit based on their AnyDeplete Technology. Needs to be tested how good/bad the capture efficiency is.

01-30-2019, 03:27 PM	#6
evan_seq24 Junior Member Location: San Diego, CA Join Date: Aug 2016 Posts: 3	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?

01-31-2019, 08:21 AM	#7
MU Core Member Location: Columbia, Missouri Join Date: Apr 2008 Posts: 57	Our group has obtained similar results with the RiboMinus kit. rRNA mapping at ~80%. Alternatives are still needed.

02-01-2019, 04:00 AM	#8
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Just to be sure do you mean 70-90% of final reads are still rRNA? @MU_Core and @evan_seq24?

02-01-2019, 05:50 AM	#9
MU Core Member Location: Columbia, Missouri Join Date: Apr 2008 Posts: 57	Yes, final reads which are rRNA.

09-17-2019, 01:04 AM	#10
furor Member Location: Europe Join Date: Jan 2012 Posts: 10	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!

11-11-2019, 06:13 PM	#13
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	Has anyone tried this kit from ZYMO? Usually ZYMO stuff is pretty good... https://www.zymoresearch.com/product...ersal-cdna-kit

11-12-2019, 04:17 AM	#15
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	Ha! Talk of the Devil! New kit by Qiagen... http://cloud.go.qiagen.com/e/es?s=87...d=6008&elqat=1

11-12-2019, 04:59 AM	#16
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Illumina is going to re-introduce ribozero equivalent kits in 2020.

11-12-2019, 06:45 AM	#17
MU Core Member Location: Columbia, Missouri Join Date: Apr 2008 Posts: 57	For those seeking a bacterial rRNA depletion kit, NEB has just released a kit that works very well in our hands. https://www.neb.com/products/e7850-n...%20Information

02-05-2020, 07:00 PM	#19
luc Senior Member Location: US Join Date: Dec 2010 Posts: 452	According to rumors, RiboZero will make a comeback. Not exactly the same products though; it will use a new chemistry.

02-06-2020, 05:12 AM	#20
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Illumina did release a new version of RiboZero+ yesterday: https://www.illumina.com/products/by...depletion.html