SEQuoia RiboDepletion Kit

Print
SEQuoia RiboDepletion Kit

Overview

Superior Preservation of the Whole Transcriptome
Rare transcripts

Depletion of rRNA after RNA-Seq library preparation enriches for RNAs of interest and preserves the diversity of the transcriptome. A, a significantly greater number of small RNAs (<200 bases) is retained using a post–library depletion strategy compared to a pre–library depletion strategy. Libraries were constructed using the SEQuoia Complete Stranded RNA Library Prep Kit (catalog #17005726) and either rRNA depleted (NEBNext rRNA Depletion Kit, New England Biolabs [NEB], #E6350L) Human Placenta Total RNA (Thermo Fisher Scientific Inc., #AM7950) or nondepleted Human Placenta Total RNA. The library constructed using nondepleted total RNA was subsequently depleted using the SEQuoia RiboDepletion Kit. Libraries were then sequenced on a NextSeq® 500 Sequencing System (Illumina, Inc.) to a read depth of 10 million. The number of unique small RNAs detected (RPKM ≥5) was significantly more in the post–library depletion sample, resulting in a more complex library and richer dataset.

 
Consistent Depletion Across A Broad Input Range
Depletion Efficiency

Effective depletion of rRNA from libraries constructed using a variety of RNA library prep kits and a broad input range. A, the SEQuoia RiboDepletion Kit effectively removes rRNA fragments from libraries constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (), Illumina® TruSeq® Stranded Total RNA Library Prep Kit (), or KAPA RNA HyperPrep Kit (Roche Sequencing, ). Each library was constructed using 100 ng of Human Placenta Total RNA according to the manufacturer’s instructions. A broad range of input cDNA (0.1–20 ng) from each library was depleted using the SEQuoia RiboDepletion Kit and sequenced to a read depth of 10 million. On average, <10% of sequencing reads map to rRNA and mt rRNA, indicating efficient and consistent depletion across a broad input range. B, transcriptome profiling is preserved when libraries are depleted in a pooled reaction. The number of total unique transcripts (RPKM >0.1) in the libraries depleted in the pooled reaction was compared to the number in the individually depleted libraries. For each library, the correlation R was >0.97. These data suggest RNA-Seq libraries can be depleted in one multiplexed reaction without compromising depletion efficiency or transcript expression. RPKM, reads per kilobase per million mapped reads; rRNA, ribosomal RNA.

 
Efficient Multiplex Depletion
Multiplexed Depletion

RNA-Seq libraries can be depleted in a 96-plex pooled reaction without affecting library quality. A, similar depletion efficiency is obtained when libraries are depleted individually compared to when they are pooled and depleted in one multiplexed reaction, even if the libraries are constructed using different library preparation kits. Ninety-six individual pre-indexed libraries were constructed using 100 ng Human Placenta Total RNA: 48 libraries were constructed using the SEQuoia Complete Stranded RNA Library Prep Kit and 48 libraries with the NEBNext Ultra II Directional RNA Library Prep Kit. An aliquot of each library was either individually depleted (singleplex) using the SEQuoia RiboDepletion Kit or pooled (multiplex) by mixing an equal molar ratio of the libraries and then depleted. Libraries were sequenced on the NextSeq 500 Sequencing System to a read depth of 3 million reads. Consistently, the percentage of reads mapping to rRNA in a library that was depleted in the multiplex reaction was comparable to those libraries that were depleted individually.

 

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.
Read full description

Ordering Information


Description

Frequently Asked Questions

SEQuoia FAQ

Learn more about how to use the SEQuoia RiboDepletion Kit.

View SEQuoia FAQs

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.

Features and Benefits

Applications and Uses

The post-library prep depletion strategy employed in SEQuoia RiboDepletion Kit is ideal for researchers

  • Working with a limited or degraded sample
  • Targeting rare transcripts
  • Generating sequencing data that is more representative of the complete transcriptome

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.

Related Products


Specifications

Technology 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

Ordering

x

Account price failed to display. Please try reloading the page.Reload Page

If you are placing an order, you may proceed with your order; the account price will be applied if it is lower than the
list price. If the problem persists, please call customer service at or send an
email to

SEQuoia RiboDepletion Kit, 24 reactions

17006487
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

List Price: 
 
$1,550.00 
LoadingLoading...
EDU Price:
 
What is this?
Your Price: 
 
LoadingLoading...
Your Price:
 

Communication error

Reload Page

Quantity:   Add to Cart
 

Accessories

x

Account price failed to display. Please try reloading the page.Reload Page

If you are placing an order, you may proceed with your order; the account price will be applied if it is lower than the
list price. If the problem persists, please call customer service at or send an
email to

0.2 ml 8-Tube PCR Strips and Domed Cap Strips, high profile, clear

TBC0802
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)

List Price: 
 
$253.00 
LoadingLoading...
EDU Price:
 
What is this?
Your Price: 
 
LoadingLoading...
Your Price:
 

Communication error

Reload Page

Quantity:   Add to Cart
 

Documents

Number Description Options
7460 SEQuoia RiboDepletion Kit Product Information Sheet Click to download
3220 Explore the SEQuoia Workflow for Revolutionized RNA Sequencing Product Information Sheet Click to download
10000132295 SEQuoia RiboDepletion Kit Protocol Click to download

This product contains electrical or electronic material. Learn more about Bio-Rad's EU Recycle Program

Get Help
Sign Up for Bio-Rad Updates!
Enter your email address below to receive your choice of the latest news, promotions, and more.