Zymo Reagents

<h2>What are RNA-seq accessories?</h2>
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RNA-seq accessories are the supporting consumables used alongside a core metatranscriptomic library preparation kit, including rRNA depletion reagents that reduce the ribosomal RNA dominating most total RNA extracts, magnetic bead-based reagents for library cleanup and size selection between preparation steps, and quantification or fragment-size quality-control tools used to confirm a library's concentration and integrity before committing it to a sequencing run.
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<h2 dir="ltr">What you will find:</h2>
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Dual-Indexed UDI Primer Sets: High-purity Unique Dual Index (UDI) primers designed to eliminate index hopping and ensure accurate demultiplexing during high-throughput NGS library preparation.
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96-Index Primer Plates: Nuclease-free, high-diversity primer configurations optimized for scalable parallel processing and the detection of rare microbial transcripts with maximum precision.
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<h2>How to choose RNA-seq accessories</h2>
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Match your rRNA depletion reagent to your sample's species complexity
A depletion reagent validated for human and common bacterial species works well for many host-associated samples, while a depletion kit specifically designed for mixed, complex bacterial populations is needed for more diverse environmental or microbiome community samples.
Use magnetic bead cleanup for size selection between library prep steps
Magnetic bead-based cleanup reagents remove unwanted small fragments and reaction components between enzymatic steps in library preparation, and the bead-to-sample ratio used can be adjusted to select for a specific fragment size range appropriate to your sequencing platform.
Confirm library quantification method matches your downstream platform requirements
A fluorometric or fragment-analysis-based quantification method provides the library concentration data needed to pool multiple samples accurately for multiplexed sequencing, and using a method appropriate to your specific library type avoids over- or under-loading the sequencer.
Check fragment size distribution before sequencing to catch problems early
Running a quality-control check of library fragment size distribution, using an instrument like a Bioanalyzer or similar fragment analyzer, helps catch a library prep problem, such as adapter dimer contamination, before committing the sample to a full sequencing run.
Plan for accessory compatibility with degraded or low-input RNA samples
Some accessories and protocols accommodate degraded RNA with low RNA integrity number (RIN) scores, such as RNA from challenging sample types, though performance may be somewhat reduced compared with high-quality, intact RNA input.
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<h2>Specifications context</h2>
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A streamlined rRNA depletion accessory can effectively deplete multiple rRNA species in a single-tube reaction, reducing the hands-on accessory steps needed compared with older multi-step depletion protocols, while still requiring downstream library cleanup and quantification accessories regardless of which depletion method is used. As of 2026, fragment analyzer and similar QC instrumentation remain a standard accessory-stage check before sequencing, helping confirm library quality issues are caught and addressed prior to committing limited sequencing capacity to a problematic sample.
<a href="https://mbpinc.net/contact-us">Contact the helpful team at MBP Inc.</a> today to request a quote for your RNA-Seq accessory needs.

RNA-seq accessories

DataSheet

Protocol

Zymo-Seq UDI Primer Plate (Indexes 1-96)

D3096 by Zymo Research provides 96 unique dual-index (UDI) primer pairs — indexes 1–96 — in a pre-formatted 96-well plate for multiplexed Illumina® NGS library preparation. Each well delivers 10 µL at 5 µM total primer concentration, compatible with TruSeq® adapter-based kits including Zymo-Seq RiboFree® and SwitchFree™. Store at -80°C.

Manufacturer

Shipping Condition

Storage Condition

MSDS

Zymo-Seq UDI Primer Set (Indexes 1-12)

D3008 by Zymo Research is the Zymo-Seq UDI Primer Set (Indexes 1–12)—12 unique dual-index primer pairs, each pre-mixed at 5 µM total (2.5 µM i5 + 2.5 µM i7) in individual 1.5 mL tubes. Compatible with the Zymo-Seq RiboFree® Total RNA and SwitchFree 3′ mRNA library kits and any Illumina TruSeq® adapter-based library kit, enabling unambiguous multiplexing of up to 12 samples on any Illumina sequencer.

<h2>What are epigenetics NGS library preparation kits?</h2>
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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).
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<h2 dir="ltr">What You Will Discover:</h2>
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<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>
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<h2>How to choose epigenetics NGS library preparation kits</h2>
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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.
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<h2>Specifications context</h2>
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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

MSDS (CA)

MSDS (EU)

MSDS (US)

Zymo-Seq WGBS Library Kit (24 Rxns.)

D5465 by Zymo Research is the Zymo-Seq WGBS Library Kit (24 Rxns.), enabling whole genome bisulfite sequencing library preparation in a single tube in ~4 hours with 10–100 ng DNA input and &gt;90% CpG site coverage across mammalian genomes. Compatible with all Illumina sequencing platforms.

DNA Input

Processing Time

Required Equipment

Required material not provided

Sequencing Platform

Plates

Zymo-Spin™ 384 Well Plate (2 Pack)

Zymo Research C2012 Zymo-Spin 384 Well Plate, polypropylene with 1.2 µm glass fiber membrane, 140 µl per well. 2-plate pack. Made in USA. For high-throughput nucleic acid purification.

<h2>What are ChIP kits?</h2>
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ChIP (chromatin immunoprecipitation) kits provide all the components needed to enrich a specific protein-DNA complex from fixed, sheared chromatin using an antibody against the protein of interest, whether a histone modification like H3K4me3 or a DNA-binding protein like a transcription factor. A complete ChIP kit covers: formaldehyde crosslinking of proteins to DNA in intact cells or tissue, cell lysis and nuclear extraction, chromatin shearing to appropriate fragment sizes, immunoprecipitation using an antibody pre-bound to protein A/G beads, sequential washing to remove non-specific binding, elution of the antibody-protein-DNA complex, de-crosslinking to release the DNA, and purification of the enriched DNA for downstream analysis.
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<h2 dir="ltr">What you will find:</h2>
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<a href="https://mbpinc.net/reagents/epigenetics/chip-kits/buffers">Buffers: </a>for immunoprecipitation, chromatin preparation, elution, and washing workflows. Includes Chromatin Shearing Buffer, MN Digestion Buffer, and Chromatin Wash Buffers, designed to support efficient chromatin cleanup, fragmentation, and recovery in ChIP assays
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<h2>How to choose and use ChIP kits</h2>
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Decide between sonication-based and enzymatic chromatin shearing
Sonication shears chromatin mechanically into fragments typically 200&ndash;1000 bp through several optimized burst-and-cool cycles, while enzymatic kits use micrococcal nuclease (MNase) or similar enzymes to cleave chromatin at accessible linker regions. Each approach has different resolution characteristics and cell-type-specific optimization requirements.
Confirm your ChIP kit is compatible with your antibody and magnetic bead format
Most modern ChIP kits use magnetic protein A or protein G Dynabeads to capture the antibody-antigen complex during immunoprecipitation, and matching the bead type to the antibody species and isotype is important for efficient capture and low background.
Plan sonication optimization as a required step before your ChIP experiment
Fragment size after sonication, ideally 200&ndash;750 bp for most ChIP-seq applications, must be confirmed by gel electrophoresis or Bioanalyzer before proceeding, since fragment size directly affects both immunoprecipitation efficiency and the resolution of the resulting ChIP-seq data.
Include an input chromatin control and an isotype control antibody
Running an aliquot of the pre-immunoprecipitation chromatin as an input control normalizes for differences in chromatin accessibility across the genome, while an isotype-matched antibody control establishes background enrichment levels above which true binding sites can be distinguished.
Keep all steps after cell lysis cold to prevent protein degradation
Chromatin prepared for ChIP is sensitive to protease activity and non-specific interactions after formaldehyde fixation, and including protease inhibitors in all lysis and wash buffers, as well as keeping samples cold throughout, reduces background and preserves specificity of the immunoprecipitation.
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<h2>Specifications context</h2>
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Sonication requires careful optimization for each cell type and instrument, typically involving pilot experiments at varying pulse widths, total times, and rest intervals, with fragment size evaluated by gel electrophoresis after de-crosslinking to confirm the target range of 200&ndash;750 bp before a full ChIP experiment is run. As of 2026, low-input and ultra-low-input ChIP kits continue to expand access to ChIP experiments from limited cell numbers such as primary cell populations and rare clinical samples, while nano-ChIP and CUT&amp;RUN approaches provide complementary alternatives for very low cell inputs where classical ChIP requires too many cells.
<a href="https://mbpinc.net/contact-us">Contact the expert team</a> at Molecular Biology Products Inc. (MBP) to get premium-quality ChIP reagents and buffers for your lab.

ChIP Kits

D5209 - MSDS

MSDS - D5210

Zymo-Spin™ ChIP Kit

Zymo-Spin ChIP Kit (D5209) by Zymo Research — 10-prep chromatin immunoprecipitation kit for mammalian cells. Combines ZymoMag Protein A bead capture with Zymo-Spin micro-elution columns (≥6 µl recovery). Suitable for ChIP-qPCR and ChIP-Seq. Made in the USA.

Applicable For

Sample Source

Storage

Zymo-Spin™ ChIP Kit (10 Preps.)

Zymo-Spin™ ChIP Kit (25 Preps.)

Spin Columns

Zymo-Spin™ I Columns

C1003-ZYM by Zymo Research — uncapped Zymo-Spin I silica columns binding up to 5 µg DNA or 10 µg RNA, with a minimum elution volume of 6 µl. A foundational column format across Zymo Research DNA and RNA purification kits, operated with standard microcentrifuges.

Binding Capacity

Compatibility

Elution Volume

Format

Matrix/Construction

Volumetric Capacity

Zymo-Spin™ I Columns (250 Pack)

Zymo-Spin™ I Columns (50 Pack)

Zymo-Spin™ I-96 Plate

Zymo Research C2004 Zymo-Spin I-96 Plate (deep-well), 2-plate pack. Silica/PP matrix; binds up to 5 µg DNA or 10 µg RNA per well; min elution ≥10 µl; 1.1 mL well capacity. 35 mm × 83 mm × 125 mm. Centrifuge compatible.

Zymo-Spin™ I-96 Plate (2 Plates)

Zymo-Spin™ I-96 Plate (Shallow-Well) (2 Plates)

Zymo-Spin™ I-96-XL Plates (2 Plates)

C2010 by Zymo Research — 2-pack of Zymo-Spin™ I-96-XL deep-well 96-well purification plates for high-throughput HMW DNA (up to 5 µg/well) and RNA (up to 10 µg/well) purification. 1.1 ml well capacity; elution in ≥ 15 µl per well. Centrifuge-compatible. Pair with Air Permeable Sealing Cover (C2011-2).

Zymo-Spin™ IB Columns

C1014-ZYM by Zymo Research are Zymo-Spin IB Columns — black opaque silica-matrix spin columns for microcentrifuge-based DNA and RNA purification. Bind up to 5 µg DNA or 10 µg RNA per column; elute in ≥6 µl from up to 800 µl sample volume. Available in 50- and 250-column packs.

Applications

Capacity

Zymo-Spin™ IB Columns (250 Pack)

Zymo-Spin™ IB Columns (50 Pack)

Zymo-Spin™ IB-96 Plate (2 Plates)

C1103-50 by Zymo Research — 50-pack of Zymo-Spin™ IC-XM silica spin columns for high molecular weight DNA (up to 5 µg) and RNA (up to 10 µg) purification on a microcentrifuge. 800 µl capacity; minimum elution volume ≥ 10 µl. Validated for use with Quick-DNA Microprep Plus Kit (D4074).

Zymo-Spin™ IC Columns

C1004-ZYM by Zymo Research are capped silica-matrix spin columns that bind up to 5 µg DNA or 10 µg RNA per column and elute in as little as 6 µl. Available in 50- and 250-column packs for microcentrifuge-based nucleic acid purification workflows.

Zymo-Spin™ IC Columns (250 Pack)

Zymo-Spin™ IC Columns (50 Pack)

Zymo-Spin™ IC-S Columns

C1082-5 by Zymo Research — 5-pack of Zymo-Spin™ V-PX Column Assemblies with 15 ml and 50 ml reservoirs for large-scale plasmid DNA purification. Binds up to 3.0 mg plasmid DNA; elutes in ≥ 300 µl. Designed as a refill for the ZymoPURE II Plasmid Gigaprep Kit. Centrifuge and vacuum manifold compatible.