SEQuoia RiboDepletion Kit

SEQuoia RiboDepletion Kit


SEQuoia RiboDepletion kit is a stand-alone kit that employs post-library depletion strategy to eliminate fragments derived from ribosomal RNA from an RNA-Seq library.

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Frequently Asked Questions


Learn more about how to use the SEQuoia RiboDepletion Kit.

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SEQuoia RiboDepletion Kit is a stand-alone, post-library depletion kit that eliminate fragments derived from cytoplasmic ribosomal RNA (rRNA) and mitochondrial ribosomal RNA (mt rRNA) sequences from an RNA-Seq library. The ribosomal RNA is abundant, constituting 80–90% of total RNA. Efficient removal of rRNA is critical to enable cost-effective sequencing of RNA samples.

Depletion of rRNA from total RNA before library construction can result in the loss of rare or low-abundance transcripts. SEQuoia RiboDepletion Kit depletes cDNA library fragments that were derived from rRNA post-library preparation, exhibiting superior performance in profiling the whole transcriptome, retaining and capturing small RNAs while minimizing the loss of rare transcripts and RNA from limited or degraded samples. This stand-alone ribodepletion kit is optimized to work with a broad input range (0.1–20 ng of RNA-Seq library) and is compatible with most available library prep kits. With the innovative post-library depletion technology, multiple pre-indexed libraries can be pooled and depleted in a single reaction, maximizing the depletion efficiency and saving significant time and cost.

The streamline workflow can be finished within 2 hours.

A Novel Technology for Post-Library Depletion Strategy

Features and Benefits

Included Components

Each kit comes with two reagent boxes. Box A includes reagents for cDNA hybridization, depletion and amplification; store at
–20ºC. Box B includes purification beads; store at 4ºC.


SEQuoia RiboDepletion Kit FAQs

SEQuoia RiboDepletion Kit Technology

What is the benefit of depleting rRNA-derived fragments after library construction?

Why does a library with small insert size have higher percent of reads mapping to rRNA?

Does the SEQuoia RiboDepletion Kit deplete cytoplasmic and mitochondrial ribosomal RNA?

SEQuia RiboDepletion Kit Compatibility

What species are compatible with the SEQuoia RiboDepletion Kit?

Can I use the SEQuoia RiboDepletion Kit with other library prep kits?

Is this product compatible with degraded or fragmented RNA?

SEQuoia RiboDepletion Kit Usage

What is the total RNA input I should use?

What is the percentage of rRNA remains after depletion using the SEQuoia RiboDepletion Kit?

Can libraries constructed using different library preparation kits be pooled into a single reaction?

How many libraries can be pooled into a single depletion reaction when using the SEQuoia RiboDepletion Kit?

Data Analysis

How can the percentage of residual rRNA be calculated using SeqSense NGS Data Analysis Software?

How do I calculate the percentage of residual rRNA using a different pipeline to process the FASTQ file?



Hybridization and capture
Input Range
0.1–20 ng cDNA (RNA-Seq library)
Compatible Species
Human / Rat / Mouse
Depleted rRNA Subtype
rRNA (5S, 5,8S, 18S, 28S), mt rRNA (12S and 16S)
Workflow Time
2 hours
Transcripts Retained
Long non-coding RNA, mRNA, miRNA, tRNA, snRNA, etc.
Shelf life
Guaranteed 12 months from shipment when properly stored




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Pkg of 1, kit for 24 reactions, includes 880 µl SEQuoia Ribodepletion Amplification Mix, 110 µl SEQuoia Ribodepletion Probe Mix, 65 µl SEQuoia Ribodepletion primers, and 2,500 µl SEQuoia Ribodepletion beads




Pkg of 20, bag of 12 x 8 thin-wall polypropylene tube strips and 12 x 8-cap strips for PCR, natural (1,920 tubes and 1,920 caps)



Number Description Options
SEQuoia RiboDepletion Kit Product Information Sheet
Explore the SEQuoia Workflow for Revolutionized RNA Sequencing Product Information Sheet
SEQuoia RiboDepletion Kit Protocol