RiboCop rRNA Depletion Kits

RiboCop HMR contains probes for the rRNA depletion of human, mouse and rat RNA samples and was also successfully tested on hamster, mini pig, and zebrafish samples.

Depending on input sample, standard recovery rate yield varies from 1 – 3%.

RiboCop HMR V2 efficiently reduces rRNA reads from 80 – 90 % down to below 1 % over a broad range of input amounts. Depending on input sample, depletion down to 1 – 2 % is standard.

RiboCop HMR is suitable for input amounts from 1 ng – 1 µg of total RNA input.

The difference between the two versions is the Probe Mix provided with the kit (HMR V2, previously PM in V1.3). In V2, a sophisticated algorithm was utilized to design efficient probes that minimize off-target effects. This new Probe Mix is designed to cover all transcript variants. The workflow and steps follow the streamlined protocol from V1.3. Additionally, enhanced depletion is achieved with V2 compared to V1.3 for both high- and low-quality RNA.

RiboCop for Human/Mouse/Rat plus Globin (HMR+Globin) was tested extensively on whole blood RNA of varying quality from human, mouse, and rat.

Globin mRNA accounts for 30 – 80 % of blood mRNA. Using RiboCop for Human/Mouse/Rat plus Globin (HMR+Globin), >90 % of the globin mRNA is efficiently removed.

This increase is expected due to the fact that 35 – 75 % of mRNA (specifically, globin mRNA) are removed. In absolute numbers, the rRNA stays the same but makes up a larger fraction of reads due to the decrease in non-rRNA fraction.

With RiboCop HMR+Globin, you will save around 2 – 4 times sequencing depth compared to rRNA depletion alone as globin mRNA accounts for 30 – 80 % of all mRNA in whole blood samples.

For rRNA depletion from Gram negative (e.g., E. Coli) or Gram positive (e.g., B. Subtilis) bacterial monocultures we recommend the RiboCop for Gram Negative or Gram Positive Bacteria kits, respectively (Cat. No. 126 or 127).

The META Probe Mix (Cat. No. 125) is primarily suited for depletion of total RNA from mixed bacterial samples (e.g., for meta-transcriptome analysis of complex communities or microbiome samples).

The recommended input range for efficient depletion with RiboCop rRNA Depletion Kits for Bacteria is 1 – 1,000 ng of total RNA for monocultures of Gram negative or Gram positive bacteria using the respective G- and G+ Probe Mixes (Cat. No. 126 and 127, respectively). We suggest initial experiments to be performed using 100 ng of input material.

The META Probe Mix (Cat. No. 125) is primarily suited for depletion of 1 – 1,000 ng of total RNA from mixed bacterial samples. The META Probe Mix may also be used at 1 – 100 ng when working with monocultures.

Processing high quality RNA from bacterial monocultures with the Gram Positive or Gram Negative Probe Mixes usually results in less than 1 % remaining rRNA reads.

Depletion rates for the META Probe Mix using RNA from mixed bacterial samples can vary depending on the sample. For specific questions please contact support@lexogen.com.

Depletion rates may vary depending on the quality of the RNA and purity of the sample. Contaminants, such as salts, metal ions and organic solvents, may have a negative impact on the efficiency of the protocol.

Yes, however the recommended input range in this case is 1 – 100 ng of total RNA.