Ribo-Zero™ rRNA Removal Kits (Human/Mouse/Rat)

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The Ribo-Zero™ rRNA Removal Kits (Human/Mouse/Rat) remove more ribosomal RNA (rRNA) from intact RNA, partially degraded RNA, and RNA isolated from formalin-fixed paraffin-embedded (FFPE) human, mouse, and rat RNA preparations than any other method.  The Ribo-Zero kits set a new standard for rRNA removal for whole-transcriptome RNA-Seq.

Benefits

  • Removes >99.9% of 28S, 18S and 5.8S rRNA, and >95% of 5S rRNA from intact, and partially degraded, including FFPE-derived, human, mouse, and rat RNA preparations (Tables 1 and 2).
  • Single-pass, 90- to 120-minute process yields RNA sufficiently depleted of rRNA for RNA-Seq (Table 2), random-primed cDNA synthesis, and other applications.
  • Recovers mRNAs and ncRNAs for whole-transcriptome RNA-Seq.
  • Preserves the transcript profile of the sample (Fig. 1 and 2).
  • Recovers both the 5´- and 3´-end fragments of mRNAs and ncRNAs in a partially degraded RNA sample, including FFPE RNA.

Applicable for use with a variety of eukaryotic species. Please inquire if your organism is not listed.

Sample Percent Removal rRNA
28S 18S 5.8S 5S
Intact HeLa total RNA >99.9% >99.9% >99.9% 96.8%
Partially degraded HeLa total RNA >99.9% >99.9% >99.9% 97.8%
Table 1. qRT-PCR analysis of rRNA removal. Intact and partially degraded HeLa total RNA were treated using the Ribo-Zero™ rRNA Removal Kit (Human/Mouse/Rat). The amount of rRNA was then determined by random-primed reverse transcription-qPCR using PCR primers to multiple regions of each rRNA. Results of several experiments were averaged.
Table 2. Expected yield of rRNA-depleted RNA. The yield of rRNA-depleted RNA is dependent on the rRNA content of the sample, the ncRNA content of the sample, and the method used for final purification of the rRNA-depleted RNA.
Ribo-Zero™ Kit Amount of Input RNA per Reaction Yield of rRNA-Depleted RNA
Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) 1-5 µg 3%-10% of input RNA
Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) Low Input 100 ng-1 µg 3%-10% of input RNA
Total RNA Sample rRNA Removal Kit % rRNA Sequences
Intact UHRR Ribo-Zero Kit 1.4%
Intact UHRR Competitive Kit 18.4%
Partially Degraded UHRR Ribo-Zero Kit 2.1%
Partially Degraded UHRR Competitive Kit 63.3%
FFPE RNA (human breast tumor) Ribo-Zero Kit Low Input 2%
Table 3. The Ribo-Zero™ rRNA Removal Kit (Human/Mouse/Rat) significantly improves RNA-Seq results. Intact and partially degraded Universal Human Reference RNA (UHRR) or human breast tumor FFPE RNA was treated with either the Ribo-Zero Kit or a competitive kit. The rRNA-depleted RNAs were used to prepare RNA-Seq libraries that were sequenced on an Illumina® GAIIx.

A B
Figure 1. High correlation of differential gene expression compared to MAQC qPCR data. RNA-Seq libraries were prepared using Epicentre's ScriptSeq™ mRNA-Seq Library Preparation Kit (Illumina®-compatible) from intact (A) or fragmented (B) UHRR and Human Brain Reference RNA (BrRR) total RNA samples, after rRNA removal using the Ribo-Zero Kit.

Figure 2 (click to enlarge). qRT-PCR analysis of rRNA removal. Intact and partially degraded UHR RNA were treated with Ribo-Zero™ Magnetic Kit (Human/Mouse/Rat). The amount of rRNA was then determined by random-primed reverse transcription-qPCR using PCR primers to multiple regions of each rRNA. Results of several experiments were averaged.

Figure 3 (click to enlarge). Gene expression correlation of Ref Seq genes. ScriptSeq™ RNA-Seq libraries were prepared from Universal Human Reference RNA (UHRR) and Brain Reference RNA (BrRR) after poly(A) enrichment or treatment with the Ribo-Zero™ Kit (Human/Mouse/Rat). The sequencing data show excellent gene expression correlation (R = 0.932).