Combination riboPOOLs

Combination riboPOOLs allow to combine up to 4 of any riboPOOL available in our portfolio. Combination riboPOOLs are recommended anytime there is the need to deplete rRNAs originating from multiple and taxonomically distant species. Table 1 includes examples of research areas were Combination riboPOOLs can be applied.

Research Area Example of Combination riboPOOLs
Human infection studies

Human riboPOOL + Pan-Bacteria riboPOOL

Human riboPOOL + Pan-Fungi riboPOOL

Zoonosis

Pan-Mammal riboPOOL + Pan-Bacteria riboPOOL

Pan-Bird riboPOOL + Pan-Bacteria riboPOOL

Plant diseases Pan-Plant riboPOOL + Pan-Fungi riboPOOL

 

Combination riboPOOLs can be ordered in two different formats:

Pre-mixed: individual riboPOOLs are mixed prior to being shipped. The combination riboPOOL is ready to use. This option is available for the following riboPOOL kit sizes: 12, 24, and 96rxn.

Separate tubes: each riboPOOL is supplied in a separate tube. Individual riboPOOLs have to be mixed before use. This option is available for the following riboPOOL kit sizes: 6 rxn trial, 12, 24, and 96rxn.

Readily available combination riboPOOLs

In addition to custom combinations, a set of pre-mixed combination riboPOOLs is also available. For these combination, ratios between the individual riboPOOLs have already been tested and optimized. All Combination riboPOOLs listed below are designed for ribodepletion in RNA-Seq experiments. If you would like to combine 2 or more of our Ribo-Seq riboPOOLs, you can use the Design Combination riboPOOL tool above. 

Combination riboPOOL Name Contains Ratio Depletes
Human Holobiont riboPOOL

Human riboPOOL

Pan-Prokaryote riboPOOL

100:1

Human rRNAs

Bacteria rRNAs

Fly Holobiont riboPOOL

Drosophila melanogaster riboPOOL

Pan-Bacteria riboPOOL

10:1

Drosophila rRNAs

Bacteria rRNAs

Mouse Microbiome riboPOOL

Mouse-Rat riboPOOL

Pan-Bacteria riboPOOL

Poly(A) riboPOOL

8:1:1

Mouse rRNAs

Mouse mRNAs

Bacteria rRNAs

Combination riboPOOLs at work

Sponges (phylum Porifera) are a ubiquitous group of invertebrates inhabiting both marine and freshwater habitats that do often form symbioses with different bacteria species. Based on the abundance of the bacterial symbionts, sponges can be classified as High Microbial Abundance (HMV) or Low Microbial Abundance (LMW)[1]. For this reason, the simultaneous depletion of both host (sponge) and symbiont (bacteria) ribosomal RNAs is often required when sequencing sponge RNA.

The Bioanalyzer profiles shown in Figure 1 and Figure 2 illustrate the ability of combination riboPOOL - in this case a 1:1 mix of Pan-Sponge and Pan-Bacteria riboPOOLs - to efficiently remove both sponge and the microbial rRNAs in a single ribodepletion step.

The gray profiles (Figure 1 and Figure 2) correspond to sponge non-ribodepleted total RNA. Here both the bacteria (23S and 16S ) and sponge (28S and 18S) rRNA peaks are evident. After depletion with the Pan-Sponge riboPOOL (Figure 1, orange profile), sponge rRNAs have been efficiently depleted, while been bacteria ribosomal RNA peaks are still noticeable. With the Combination riboPOOL however, depletion of sponge rRNAs is accompanied by the concurrent removal of bacterial rRNAs (Figure 2, orange profile).

Figure 1 Bioanalyzer profiles of demosponge Lendenfeldia chondrodes total RNA before and after depletion with Pan-Sponge riboPOOL.

[1] Hentschel, U. et al. (2003). Microbial diversity of marine sponges. Prog. Mol. Subcell. Biol. 37, 59–88. 

Figure 2 Bioanalyzer profiles of demosponge Lendenfeldia chondrodes total RNA before and after depletion with the Combination riboPOOL: Pan-Sponge and Pan-Bacteria riboPOOL.

Publications

A study by Fritz et al. (2022) focused on obtaining host and bacterial RNA sequences from infected human tissues using dual, host-pathogen RNA sequencing to better understand the relationship between ulcer infections severity and clinical classifications.

Combination riboPOOL: Human:Pan-Prokaryote riboPOOL (100:1)

Read more on the siTOOLs Biotech blog.

What customers say

"We are a group at the LMU in Munich working with sponges and their microbiomes. We always had problems finding a good solution to economically perform rRNA depletion for these complex holobionts and sequence their metatranscriptomes. siTOOLs Biotech has designed and produced a Pan-Sponge riboPOOL for ribodepletion in sponges. Since we can combine different siTOOLs Biotech riboPOOLs, we can co-deplete sponge and bacterial rRNAs in one shot without losing any important transcriptomic information. This has opened new possibilities to study sponge holobionts in a more integrated manner."

Dr. Sergio Vargas (Assistant Professor, Department of Earth and Environmental Science, Ludwig-Maximilians-Universität München, Germany) Publication: Vargas et al. (2022) bioRvix used the combination riboPOOL: Pan-Sponge: Pan-Bacteria.