Product Overview
In total RNA sequencing, ribosomal RNA makes up most of the RNA in a sample, so unless it is removed, most sequencing reads are spent on it. Degraded samples add a second problem. RNA from FFPE tissue usually contains a higher proportion of ITS/ETS (the transcribed spacer regions of the 45S pre-rRNA) than fresh tissue, and these fragments also consume reads. The Hyaseq rRNA & ITS/ETS Depletion Kit (Human/Mouse/Rat) is designed to remove rRNA and 45S ITS/ETS from human, mouse, and rat total RNA using an RNase H-based workflow, and to retain mRNA and other non-coding RNA. Unlike poly(A) enrichment, depletion keeps the non-polyadenylated RNA species in the library. The kit works with both intact and partially degraded RNA samples, including FFPE RNA. Because degraded FFPE samples carry more ITS/ETS, the kit includes probes in the human 45S ITS/ETS region, and ITS removal can significantly increase the proportion of valid data in the raw sequencing data. It supports a wide input range of 100 ng to 1 μg of total RNA and achieves >95% removal of rRNA, ITS, and ETS from human, mouse, and rat samples. In stability testing, removal efficiency was maintained after the reagents were stored at 4°C (3 days, and 11 days in a separate test), comparable to freshly prepared reagents. Strict batch-to-batch performance and stability controls support reliable results. Depleted RNA can go directly into RNA library preparation, including strand-specific protocols. Typical applications include gene expression research, alternative splicing analysis, detection and discovery of non-coding RNA, identification of alternative polyadenylation sites, and fusion gene detection.
Product Features
- Removes rRNA and ITS/ETS, with strong performance on FFPE samples: Probes in the human 45S ITS/ETS region are included alongside rRNA probes, which matters for degraded FFPE RNA, where ITS/ETS fragments are more abundant and would otherwise take up sequencing reads.
- >95% removal across human, mouse, and rat: The kit achieves more than 95% removal of rRNA, ITS, and ETS in samples from all three species, and keeps mRNA and other non-coding RNA for transcriptome-wide analysis.
- Wide input range with consistent quality: It supports 100 ng to 1 μg of total RNA, and strict batch-to-batch performance and stability controls give reliable, reproducible results.
FAQ
Q1: What does this kit remove, and what does it keep?
The kit removes rRNA and the 45S ITS/ETS regions from human, mouse, and rat total RNA. It keeps mRNA and other non-coding RNA, so the resulting library can capture both polyadenylated and non-polyadenylated transcripts. In an RNase H-based workflow, probes complementary to the target RNA hybridize to it, and RNase H then degrades the RNA in the hybrids.
Q2: What sample types and RNA input amounts is the kit suitable for?
The kit works with both intact and partially degraded RNA, including FFPE RNA, and supports an input range of 100 ng to 1 μg of total RNA. It is validated for human, mouse, and rat samples.
Q3: Why does ITS/ETS removal matter for FFPE and degraded samples?
Degraded FFPE samples usually contain a higher proportion of ITS/ETS than fresh tissue samples. If these regions are not removed, they use up sequencing reads. Because this kit adds probes in the human 45S ITS/ETS region, removing the ITS can significantly increase the proportion of valid data in the raw data.
