Zymo Reagents

Tubes

Zymo Research Collection Tubes

Zymo Research C1001 Collection Tubes, 2 mL polypropylene. For use with Zymo-Spin I, II, IIC, IIC-XLR, IV, and V spin columns. Available as C1001-50 (50-pack), C1001-500 (500-pack), or C1001-1000 (1000-pack). Made in USA.

Manufacturer

Shipping Condition

Storage Condition

Collection Tubes (1000 Pack)

Collection Tubes (50 Pack)

Collection Tubes (500 Pack)

Columns, Plastics & Accessories

Zymo Research Conical Reservoir

Zymo Research 15 mL Conical Reservoir C1031-25 is a polypropylene, luer-lock-compatible reservoir for DNA and RNA purification with vacuum manifold systems, designed for use with Zymo-Spin™ V-style column assemblies. Supplied as a pack of 25.

Compatibility

Matrix/Construction

Volumetric Capacity

15 ml Conical Reservoir (25 Pack)

50 ml Conical Reservoir (25 Pack)

600 ml Reservoir (5 Pack)

Zymo Research Sterile Collection Swab

Zymo Research C1052-50 sterile nylon flocked collection swab. 6-inch swab; 20 mm break point; individually wrapped. 50 swabs per pack. Room temperature storage; 13-month shelf life. Compatible with Zymo Research DNA/RNA Shield Collection Tubes. Made in USA.

Zymo Collection Swab, 20 mm break point (50 Pack)

Zymo Collection Swab, 80 mm break point (50 Pack)

Zymo ResearchAir Permeable Sealing Cover

C2011-2 by Zymo Research — 2-pack of Air Permeable Sealing Covers for 96-well microcentrifuge spin-column and collection plates. Allows gas exchange while preventing cross-contamination and reducing evaporation during incubation steps. Compatible with Zymo-Spin I-96-XL Plates (C2010). Also available in 4-pack (C2011-4) and 8-pack (C2011-8).

Air Permeable Sealing Cover (2 Pack)

Air Permeable Sealing Cover (4 Pack)

Air Permeable Sealing Cover (8 Pack)

<h2>What are epigenetics NGS library preparation kits?</h2>
&nbsp;
Epigenetics NGS library preparation kits convert the DNA output of an upstream epigenetics workflow into an indexed sequencing library: adapters are ligated to the ends of each DNA fragment, an optional amplification step increases the total amount of library, and indexes are added to allow multiplexed sequencing of many samples in a single run. These kits are specifically optimized for epigenetics-specific inputs, including ChIP-enriched DNA (often low-yield, sheared to 200&ndash;750 bp), chromatin-accessible DNA from ATAC-seq (also low-yield and fragmented), and bisulfite-converted DNA (fragmented and chemically modified, with low-complexity sequence).
&nbsp;
<h2 dir="ltr">What You Will Discover:</h2>
&nbsp;
<ul>
<li dir="ltr">Groundbreaking single-tube processes that integrate bisulfite conversion and library preparation to chart entire genomes with extremely low input needs.</li>
<li dir="ltr">Rapid, efficient transposase-driven methods that seize open chromatin areas and dynamic regulatory environments in only a few hours.</li>
<li dir="ltr">Enzymatic restriction methods combined with targeted sequencing for affordable, high-density CpG coverage without incurring full-genome expenses.</li>
<li dir="ltr">Advanced multi-adapter ligation techniques designed to reduce bias and optimize library retrieval from fragmented or challenging DNA sources.</li>
<li dir="ltr">Post-bisulfite library preparation systems designed explicitly for sub-nanogram DNA quantities, individual cells, or extensively degraded specimens.</li>
<li dir="ltr">Locus-specific, genome-wide enrichment approaches aimed at accurately monitoring and characterizing 5-hydroxymethylcytosine alterations throughout the genome.</li>
</ul>
&nbsp;
<h2>How to choose epigenetics NGS library preparation kits</h2>
&nbsp;
Match your library prep kit to your specific epigenetics input type
ChIP-seq library prep kits are optimized for low-yield sheared chromatin enriched by immunoprecipitation, while ATAC-seq kits work with tagmented open chromatin fragments, and bisulfite or enzymatic methyl-seq library prep kits are specifically formulated for the highly fragmented, low-complexity sequence characteristics of bisulfite-converted DNA input.
Confirm the kit supports your input DNA amount
ChIP experiments, especially those targeting low-abundance transcription factors or run from limited cell numbers, often yield very little enriched DNA, and kits validated for low-input or picogram-scale library preparation are necessary to generate libraries with sufficient complexity without excessive PCR amplification introducing duplicates.
Choose an indexing strategy appropriate to your sample multiplexing plan
Dual-index strategies, using unique combinations of two distinct index sequences per sample, provide more reliable sample demultiplexing in highly multiplexed runs compared with single-index strategies, and confirming whether your kit supports the number of samples and multiplexing depth required is an important selection criterion.
Understand the impact of PCR cycles on library complexity and duplicate rate
Fewer PCR amplification cycles reduce the proportion of duplicate reads in sequencing data, which is especially important for low-complexity epigenetics libraries where overamplification can dominate output with copies of the same original fragment. Efficient ligation chemistry that increases library yield from low input helps minimize required PCR cycles.
Confirm kit compatibility with your downstream analysis pipeline
Some library prep protocols use specific adapter sequences or library structures that require corresponding adjustments in bioinformatics analysis pipelines, and confirming compatibility before sequencing helps avoid downstream analysis failures.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
ChIP-seq library prep kits optimized for low-input or ultra-low-input chromatin are designed to achieve high library complexity from picogram-scale DNA inputs that would otherwise produce low-complexity libraries with standard kits at similar PCR cycle numbers. As of 2026, library prep kits compatible with enzymatic methyl-seq (EM-seq) as well as classical bisulfite-converted DNA continue to expand, enabling researchers to leverage improved DNA quality while maintaining familiar downstream sequencing workflows.
Prepared to enhance your sequencing efficiency? Discover our complete selection of NGS Library Preparation Kits and <a href="https://mbpinc.net/contact-us">contact the MBP team</a> for a quote now.

NGS Libray Preparation Kits

DataSheet

MSDS

Protocol

Zymo-Seq ATAC Library Kit (12 Rxns.)

D5458 by Zymo Research prepares 12 ATAC-seq libraries from 50,000 cells (&gt;80% viability) using a Tn5 transposase to insert sequencing adapters at open chromatin regions. Libraries in the 200–700 bp range are compatible with Illumina HiSeq, NextSeq, and NovaSeq. Twelve unique UDI Tag Primers are included for multiplexed sequencing runs.

DNA Input

Equipment Required

Library Storage

Processing Time

Reagents Not Provided

Sequencing Platform Compatibility

<h2>What are methylation standards?</h2>
&nbsp;
Methylation standards are defined reference DNA materials with a known and confirmed methylation status, ranging from a fully methylated DNA (where every cytosine at CpG or other sites carries a methyl group) to a fully unmethylated DNA (where no cytosines are methylated) and intermediate or mixed standards containing a defined ratio of the two. The most widely used unmethylated control in bisulfite sequencing is lambda phage DNA, which is naturally unmethylated and can be spiked into a conversion reaction to estimate conversion efficiency.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">Methylated and non-methylated DNA control sets for comparative epigenetic analysis and assay validation</li>
<li dir="ltr" role="presentation">Universal methylated DNA standards for methylation assessment workflows</li>
<li dir="ltr" role="presentation">Genomic DNA reference materials: for microbial and human methylation studies</li>
<li dir="ltr" role="presentation">Matched DNA sets: used in experimental models for controlled comparison of methylation status&nbsp;</li>
<li dir="ltr" role="presentation">Bisulfite-converted DNA standards: for downstream sequencing-based methylation and PCR analysis</li>
<li dir="ltr" role="presentation">Methylation spike-in controls: for sequencing normalization and high-throughput workflows</li>
<li dir="ltr" role="presentation">Mouse and human DNA methylation reference sets: for specific species epigenetic studies</li>
<li dir="ltr" role="presentation">Methylated DNA IP control kits for methylation assays involving immunoprecipitation</li>
</ul>
&nbsp;
<h2>How to use methylation standards</h2>
&nbsp;
Spike an unmethylated control into every bisulfite or enzymatic conversion reaction
Running an unmethylated DNA like lambda phage DNA alongside your samples in the same conversion reaction estimates the conversion efficiency of that specific run, since every remaining cytosine signal after conversion should be treated as a false positive, and this rate can be quantified and accounted for in downstream analysis.
Run a fully methylated positive control to confirm methylated cytosines are preserved
A fully methylated standard, such as DNA synthesized with 5-methyl-dCTP or commercially prepared methylated genomic DNA, confirms your conversion workflow correctly preserves methylated cytosines intact rather than inadvertently converting them, which would produce false-negative methylation calls.
Use a mixed or intermediate standard to calibrate quantitative methylation assays
A standard containing a defined ratio of methylated to unmethylated DNA, or a set of standards spanning a range of methylation percentages, provides a calibration curve for quantitative methylation assays like 5-methylcytosine ELISA, validating that the assay reports the expected methylation level across its full dynamic range.
Confirm standard stability before long-term storage or lot-to-lot use
Methylation control DNA has documented stability windows, and confirming that your standard's methylation status is stable under storage conditions, and consistent across lots, is necessary for reliable longitudinal monitoring of conversion efficiency.
Use standards to monitor workflow consistency over time
Running a conversion control in every batch allows longitudinal tracking of conversion efficiency across instrument runs, reagent lots, and protocol variations, helping catch workflow drift before it affects real sample results.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
Lambda phage DNA is the most commonly used unmethylated bisulfite conversion control because it is naturally unmethylated, commercially available, and well characterized, and it can be aligned to the known lambda phage reference genome after sequencing to calculate residual unconverted cytosine rates, providing a direct, interpretable measure of conversion efficiency. As of 2026, fully methylated and fully unmethylated standard sets are also used alongside enzymatic methyl-seq conversions to confirm that EM-seq's enzymatic mechanism correctly protects methylated cytosines and converts unmethylated ones, independent of the conversion chemistry used.
This category sits within DNA/RNA Methylation, alongside Bisulfite Conversion Kits, Non-Bisulfite Kits &amp; Reagents, and ELISA Kits &amp; Reagents. See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us">Contact the expert team of Molecular Biology Products Inc. (MBP)</a> to get high-quality methylation standards for your lab today.

Methylation Standards

Zymo-Seq Methyl Spike-in Control

D5500 by Zymo Research is the Zymo-Seq Methyl Spike-in Control, containing six synthetic amplicons (180–200 bp) at 0%, 10%, 25%, 50%, 75%, and 100% cytosine methylation for monitoring bisulfite conversion efficiency in WGBS and RRBS workflows. Provides 25 preparations at 60 pg/µl; store at -20°C. Research use only.

Concentration

Amplicon # 1 Methylation Level

Amplicon # 2 Methylation Level

Amplicon # 3 Methylation Level

Amplicon # 4 Methylation Level

Amplicon # 5 Methylation Level

Amplicon # 6 Methylation Level

Source

Storage

Zymo-Seq RRBS Library Kit

The D5460 by Zymo Research is a 24-prep all-in-one RRBS library prep kit for DNA methylation profiling at single-nucleotide resolution, accepting 10–500 ng genomic DNA input with ~2 hours hands-on time and ≥70% CpG island coverage. Includes Unique Dual Index (UDI) primers and is compatible with all Illumina platforms except HiSeq X Series.

Input

Sample Sources

Sequencing Platform Compatible

Zymo-Seq RRBS™ Library Kit (24 Preps.)

Zymo-Seq RRBS™ Library Kit (48 Preps.)

<h2>What are Magnetic Bead Total RNA Extraction Kits?</h2>
&nbsp;
Magnetic bead total RNA extraction kits isolate total RNA by adsorbing nucleic acids onto paramagnetic silica-coated beads in a high-chaotropic-salt lysis buffer, then using a magnetic field to capture and wash beads without centrifugation. Unlike standard spin-column kits, the bead format removes centrifuge dependency, enabling scalable manual processing in 96-well plates or full automation on liquid-handling robots.&nbsp;Choose a magnetic bead format when your lab processes more than 48 samples per day or when a Tecan, Hamilton, or Beckman Biomek platform is available.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Magbio HighPrep Kits for liquid biopsy collection systems and non-invasive swabbing using rapid magnetic bead isolation&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Zymo-Seq RiboFree&trade; Kits to eliminate ribosomal RNA carryover during library synthesis
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Direct-zol-96 MagBead RNA Modules facilitate complete avoidance of manual phase-separation steps while enabling automated transcript extraction directly from TRIzol&reg; lysates&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Magbio HighPrep Total RNA Plus Kit extracts pure, inhibitor-free RNA from complex samples with maximum binding capacity&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Quick-RNA MagBead Packs deliver high-integrity total transcripts without dependence on centrifuge spins or vacuum manifold.
</li>
</ul>
&nbsp;
<h2>How to Choose a Magnetic Bead Total RNA Extraction Kit</h2>
&nbsp;
Automation Compatibility
Confirm that the kit supplier provides automation scripts for your specific platform. The Zymo Research Quick-DNA/RNA Viral MagBead kit and Thermo Fisher MagMAX-96 both offer downloadable instrument scripts for Tecan and Hamilton systems. Generic magnetic bead kits without published automation protocols require in-house script development, adding significant setup time.
Small RNA Retention
Bead kits that bind RNA &gt;=17 nt co-purify microRNAs alongside mRNA and rRNA from the same input. Kits specifying &gt;=200 nt retention exclude small RNAs and are not appropriate for miRNA expression panels. Check the size cutoff stated in the kit datasheet before selecting for non-coding RNA work.
Input Sample Type
Magnetic bead kits for total RNA support cell pellets, tissue homogenates, blood, bacteria, yeast, and fungi. For cell-free matrices (plasma, serum, nasal wash), switch to a viral-RNA or liquid-biopsy magnetic bead kit with included carrier RNA to maximize recovery from low-input, cell-free samples.
Elution Volume and Concentration
Standard magnetic bead kits elute into 50-100 ul; some protocols allow concentration into 20-50 ul, increasing RNA concentration for sensitive downstream applications. If downstream libraries require &gt;=200 ng/ul input, reduce elution volume accordingly and verify the kit supports this protocol variant.
gDNA Removal
Confirm whether the kit includes on-bead DNase I or requires a separate gDNA digestion step. For RT-qPCR and RNA-seq, omitting DNase treatment introduces a genomic DNA signal that inflates expression measurements.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
RNA purity targets from magnetic bead extractions match spin-column benchmarks: A260/A280 &gt;= 1.8 and A260/A230 &gt;= 1.5. RNA integrity number (RIN) &gt;= 7 is recommended for RNA-seq library preparation; magnetic bead kits produce RIN values in the 8-10 range for fresh samples when lysis is performed immediately on ice. Bead-based workflows are cited in published automation protocols from genomics core facilities and are increasingly specified by NIH-funded projects requiring standardized sample processing across multi-site studies.
<section class="mbp-contact-cta"></section>
&nbsp;
<a href="https://mbpinc.net/contact-us">Contact the expert team </a>at MBP Inc. to get automation-compatible mag bead selections today.

Mag Beads

R3000-MSDS

R3000-Protocol

Zymo-Seq RiboFree™ Total RNA Library Prep Kit

R3000 by Zymo Research is a total RNA library prep kit combining probe-free RiboFree™ rRNA depletion with stranded library construction in approximately 4 hours from 10–250 ng input. The enzymatic depletion requires no species-specific probes. Academic researchers running multi-species transcriptomics or FFPE RNA-seq benefit from validated protocols covering human, mouse, rat, E. coli, Arabidopsis, and low-input samples down to 1 ng.

Equipment Needed (user provided)

Input Quality

RNA Input

Sample Input Material

Zymo-Seq RiboFree™ Total RNA Library Prep Kit (12 Preps.)

Zymo-Seq RiboFree™ Total RNA Library Prep Kit, 96 Rxns

<h2>What Are Total RNA Isolation Kits?</h2>
&nbsp;
Total RNA isolation kits are complete reagent systems that capture all RNA species present in a biological sample - including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), and small non-coding RNAs including microRNA (miRNA &gt;=17 nt) - in a single purification pass. This distinguishes them from mRNA-only kits (which use oligo-dT capture to select polyadenylated transcripts) and from small RNA kits (which use size fractionation to enrich miRNA and siRNA). Standard mini-format kits process samples of 5-100 mg tissue or 1x10^4-1x10^7 cells and yield 1-100 ug of total RNA with A260/A280 ratios of 1.8-2.1 and RIN scores &gt;=8 from fresh or properly snap-frozen material.&nbsp;Total RNA kits are the correct choice for any workflow where the complete transcriptome is needed - RNA-seq, whole-transcriptome microarray, or small RNA co-profiling - rather than a specific RNA fraction.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/rna-extraction-kits/total-rna/spin-column">Spin-column:</a> for rapid, centrifugal transcript purification utilizing advanced silica membranes&nbsp;
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/rna-extraction-kits/total-rna/96-well-plate">96-well plate:</a> for parallel and high-throughput isolation of&nbsp;cellular RNA
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/rna-extraction-kits/total-rna/mag-beads">Mag Beads: </a>for flexible and automated transcript recovery using superparamagnetic particles
</li>
</ul>
&nbsp;
<h2>How to Choose Total RNA Isolation Kits</h2>
&nbsp;
Sample Type and Lysis Method
Cultured cells and soft tissues (liver, brain, kidney) lyse efficiently in standard guanidinium isothiocyanate (GITC) or proprietary lysis buffers; no additional disruption is required. Fibrous tissues (skeletal muscle, heart, cartilage, plant material) require mechanical disruption via bead mill homogenizer (e.g., TissueLyser, BeadBug) or rotor-stator before the lysis buffer contacts the sample. Bacteria and yeast require specialized lysis conditions including enzymatic cell-wall digestion or bead beating at higher intensity. FFPE tissue sections need deparaffinization with xylene or substitute and extended proteinase K digestion; select kits explicitly validated for FFPE.
Small RNA Co-Purification
Total RNA kits differ in their ability to retain small RNA species (17-200 nt). Kits with a unique binding buffer chemistry - such as Zymo Research Quick-RNA kits - capture miRNA alongside large RNA in the same column pass. Conventional silica-column kits with high-ethanol wash steps often wash away RNA species under 200 nt. If your experiment requires miRNA detection (RT-qPCR for specific miRNAs, or small RNA sequencing), confirm the kit's small RNA retention profile before ordering.
DNase Digestion
On-column DNase I digestion is included with most total RNA kits and removes genomic DNA contamination during the wash stage. If the kit does not include DNase, a separate in-solution DNase I treatment (15-30 min at 37C) must follow elution for gene expression applications where gDNA amplification would interfere. Include on-column DNase kits for RT-qPCR and RNA-seq; the treatment adds fewer than 15 minutes to the protocol.
Binding Capacity and Sample Scale
Mini-format kits bind up to 100 ug total RNA and are adequate for most cell and tissue inputs. Midi or maxi kits are available for large tissue samples (&gt;100 mg). For micro-scale inputs (single cells, laser-capture microdissection sections, needle biopsies), use micro-format kits with 10-30 uL elution volumes to maximize concentration.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
Total RNA integrity is expressed as RIN (RNA integrity number, 1-10 scale; measured on Agilent Bioanalyzer 2100 or 4150 TapeStation). RNA-seq and microarray applications typically require RIN &gt;=7; single-cell or FFPE workflows often proceed with RIN 3-6 using short-amplicon RT-qPCR assays. Purity thresholds: A260/A280 1.8-2.1; A260/A230 &gt;1.8. Zymo Research Quick-RNA kits are among the most frequently cited total RNA isolation kits in published molecular biology methods.
<section class="mbp-contact-cta">
&nbsp;
MBP's specialist team can help match kit chemistry, format, and throughput to your sample type and downstream application.&nbsp;<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> for personalized guidance.
</section>

Total RNA

Zymo-Seq RiboFree™ Universal cDNA Kit (12 Preps.)

Zymo-Seq RiboFree™ Universal cDNA Kit (R3001) by Zymo Research prepares NGS-grade rRNA-depleted cDNA from 10–1,000 ng total RNA in 1.75 hours using probe-free universal depletion that works across mammalian, plant, bacterial, yeast, and FFPE samples. Outputs single-stranded cDNA ready for any compatible library prep method. 12-prep format.

Zymo-Seq Wash Buffer (48 ml)

Zymo-Seq Wash Buffer (6 ml)

Zymo-Seq SPLAT DNA Library Kit (12 Preps)

D5464 Zymo-Seq SPLAT DNA Library Kit by Zymo Research — 12 preps, 1–500 ng input, cfDNA, FFPE, and genomic DNA, all Illumina platforms, ~3 hours, 12 unique dual indexes.

Sample Input Type

Minimum Input

Maximum Input

Total Processing Time

Hands-On Time

Barcode Sequences

<h2>What Is RNA Sequencing?</h2>
&nbsp;
RNA sequencing (RNA-seq) uses next-generation sequencing to profile the transcriptome -- the complete set of RNA molecules produced by a cell or tissue at a given time. Ribosomal RNA (rRNA) comprises over 90% of total cellular RNA and generates no useful transcript information in standard transcriptomics experiments; its removal is therefore the key step that differentiates RNA-seq library prep approaches. The two primary enrichment strategies are poly-A selection (oligo-dT capture of polyadenylated mRNA, compatible with high-quality RNA) and ribosomal RNA depletion (removal of rRNA using hybridization probes, antisense oligonucleotides, or probe-free enzymatic depletion, compatible with degraded, FFPE, or non-polyadenylated RNA). Stranded (directional) library preparation preserves the strand orientation of each transcript during cDNA synthesis, enabling disambiguation of overlapping sense/antisense transcripts and more accurate quantification of antisense lncRNAs and imprinted gene clusters. Choose your RNA-seq kit based on RNA input amount, sample quality (RIN or DV200), organism (model vs. non-model), whether non-coding RNA information is needed, and downstream analysis goals (quantification, isoform, de novo assembly).
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" aria-level="1">
SwitchFree&trade; 3&prime; mRNA Libraries: Cutting-edge kits such as the Zymo-Seq series that attach adapters directly to first-strand cDNA, shortening library prep duration to around 4 hours and minimizing manual reagent handling.
</li>
<li dir="ltr" aria-level="1">
High-Resolution Quantification: Systems equipped with Unique Molecular Identifiers (UMIs) for precise deduplication, along with compatibility for just 10 ng of total RNA, enabling thorough high-throughput gene counting without prior mRNA enrichment.
</li>
</ul>
&nbsp;
<h2>How to Choose RNA-Seq Library Prep Kits</h2>
&nbsp;
mRNA-seq vs. total RNA-seq
mRNA-seq (poly-A selection) starts with 25 ng-1 microgram of high-quality total RNA (RIN above 7 recommended) and produces libraries enriched for protein-coding polyadenylated transcripts, delivering higher read depth per expressed gene. It is the most commonly requested RNA-seq type for differential gene expression (DGE) studies of model organisms. Total RNA-seq (rRNA depletion) accepts 10 ng-1 microgram of total RNA, accommodates lower-quality RNA (RIN above 3, DV200 above 30%), and captures both coding and non-coding RNA, including lncRNA, eRNA, pre-mRNA, and mitochondrial RNA -- critical for FFPE tissues, bacteria, or non-model organisms without polyadenylated mRNAs.
rRNA depletion technology: probe-based vs. probe-free
Traditional rRNA depletion uses biotinylated antisense oligonucleotide probes to hybridize and magnetically deplete specific rRNA species. This approach requires species-specific probe sets (human/mouse/rat, plant, bacteria) and cannot efficiently deplete rRNA from non-model organisms or mixed samples. Zymo Research's RiboFree technology uses a probe-free enzymatic approach that depletes rRNA by using the input RNA as its own template for reverse transcription, generating cDNA from highly abundant sequences and enzymatically removing them -- making it universally compatible with RNA from any organism (human, animal, plant, bacteria, virus, environmental samples) without requiring species-specific probes.
Strand specificity
Stranded (directional) RNA-seq is now the standard for most applications because it preserves transcript orientation, allowing sense and antisense transcripts to be distinguished, improving mapping accuracy in regions of overlapping transcription, and enabling quantification of antisense lncRNAs. Most modern RNA-seq kits, including Zymo-Seq RiboFree, are strand-specific by default. Non-stranded (unstranded) protocols are used only in specialized contexts requiring older analysis pipelines or specific applications.
Low-input and single-cell RNA-seq
Low-input RNA-seq kits accept 1-100 ng of total RNA using template-switching reverse transcriptases that generate full-length cDNA from limited input. Ultra-low-input kits using SMART-Seq chemistry accept 10 pg-5 ng, suitable for flow-sorted cell populations or laser-capture microdissected tissue sections. Single-cell RNA-seq (scRNA-seq) using droplet microfluidics (10x Genomics Chromium) or plate-based methods captures transcriptomes from individual cells, generating library prep inputs of 0.1-10 pg per cell.
FFPE RNA-seq
FFPE-preserved tissues yield degraded RNA with low RIN values (often below 3). RNA-seq from FFPE requires rRNA depletion (poly-A selection is not effective on degraded RNA), FFPE-optimized reverse transcriptases that handle short, damaged templates, and input quality assessment by DV200 (percentage of RNA fragments above 200 nucleotides). Samples with DV200 above 30% are generally processable with rRNA depletion kits; below 30%, recovery and data quality decline substantially.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
RNA quality is assessed by RNA Integrity Number (RIN, scale 1-10 on Bioanalyzer; 10 is intact) or DV200 (percentage of fragments above 200 nucleotides; used when RIN is uninformative for degraded samples). The standard sequencing depth for differential gene expression mRNA-seq is 20-30 million paired-end reads per sample (150 bp x 2 on Illumina NovaSeq); total RNA-seq typically requires 25-50 million reads per sample due to residual rRNA reads even after depletion. Zymo-Seq RiboFree Total RNA Library Kit depletion efficiency reduces rRNA reads to below 5% of total reads across human, mouse, plant, bacterial, and mixed samples, validated across 150+ peer-reviewed studies cited on the product page. Direct RNA sequencing on Oxford Nanopore Technologies (without reverse transcription) has emerged as a research tool for detecting RNA base modifications (m6A, pseudouridine) and native poly-A tail lengths in addition to sequence, though library prep inputs require 10 micrograms or more of polyadenylated RNA.&nbsp;
&nbsp;
Enhance your transcriptomic studies&mdash;<a href="https://mbpinc.net/contact-us">reach out to the MBP team</a> now for a quote on our expert RNA-seq library services.

RNA Sequencing

RNA-seq

Zymo-Seq SwitchFree 3′ mRNA Library Kit

Zymo-Seq SwitchFree 3′ mRNA Library Kit by Zymo Research prepares UMI-barcoded 3′ mRNA libraries from 10–500 ng total RNA (RIN ≥ 8) in ~4 hours. Compatible with Illumina and Element AVITI platforms. Includes RT reagents with built-in UMIs, adapter ligation, UDI primers 1–12, Select-a-Size beads, and ZymoTaq PreMix. Available in 12-prep (R3008) and 96-prep (R3009) formats.

Zymo-Seq SwitchFree 3′ mRNA Library Kit (12 Preps.)

Zymo-Seq SwitchFree 3′ mRNA Library Kit (96 preps)

D5462 - MSDS

D5463 - MSDS

D5462-Protocol

Zymo-Seq Trio WGBS Library Kit

Zymo-Seq Trio WGBS Library Kit (D5462) by Zymo Research — 24-prep kit for whole genome bisulfite sequencing library preparation from 5–10 ng cfDNA, FFPE, or sheared genomic DNA. Greater than 99.5% bisulfite conversion efficiency; ~6 hours total processing; compatible with all Illumina platforms. Made in the USA.