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cDNA Synthesis & Library Construction

Products >  cDNA_Synthesis_and_Library_Construction >  NGS_Automation >  Library_Prep_Automation >  In-Tip_Bead_Separation

Tech Note: Ligation-Free ChIP-Seq Library Preparation

Maximize Sample Recovery with In-Tip Bead Separation

Manual NGS library preparation for DNA-seq and RNA-seq is time-consuming and subject to human error. The automated SMARTer Apollo system provides a complete, walkaway solution for these applications, producing consistent libraries in as little as 30 minutes of hands-on time. The SMARTer Apollo system combines in-tip bead separation, prealiquoted SMARTer PrepX kits, and validated protocols for reliable sample preparation, cleanup, and NGS library prep.

Bioanalyzer traces of libraries produced from different deck positions

Increase reproducibility with in-tip bead separation

NGS library prep protocols require several bead cleanup steps that can result in variation and decreased yields due to loss of product. The SMARTer Apollo system improves bead cleanup with in-tip bead separation, which minimizes variation and product loss. Improved bead cleanup is facilitated by an automated magnetic bar. First, the SMARTer Apollo system draws up the suspended beads. Then, the magnetic bar swings down and comes into contact with the tips, instantly aggregating the beads, which can be seen as a dark mass adhering to the side of the tip that makes contact with the magnetic bar. Any remaining beads are captured by repeatedly passing the solution in the tip past the magnetic bar. After capture, the solution is cleared, and the beads can be seen as a dark mass adhering to the magnetic bar. See in-tip bead purification in action:


Automated in-tip bead capture on the SMARTer Apollo system is consistent, regardless of deck position or time of sample processing. To verify this, DNA-seq libraries were prepared on the system from E. coli DNA using the SMARTer PrepX Complete ILM 32i DNA Library Kit, 96 Samples. Bioanalyzer traces of libraries produced from different deck positions and on different days with the same input sample demonstrate consistent library preparation, independent of when the sample is processed or which deck position is used for processing.

Bioanalyzer traces of libraries produced from different deck positions

Automate SMART-Seq v4 ultra-low-input RNA-seq library prep

What do you get when you combine the industry-leading sensitivity of SMART-Seq v4 ultra-low-input cDNA synthesis with the reliability of SMARTer Apollo instrumentation? A high-throughput, automated workflow for ultra-low-input and single-cell RNA-seq that does not sacrifice quality or consistency as compared to manual methods and that frees you up to perform other experiments.

The SMART-Seq v4 Reagent Kit for the SMARTer Apollo System is designed to generate high-quality, full-length cDNA directly from 1–1,000 cells or 10 pg–10 ng of total RNA using a high-throughput workflow that enables processing of up to 96 samples in a single working day. The adaptation of our SMART-Seq v4 technology for automated library preparation provides results with high similarity to those of manually generated libraries while minimizing variation and hands-on time.

High correlation between libraries generated from manual and automated cDNA amplification samples

Reduce errors with complete, plug-and-play SMARTer PrepX kits

Manual NGS library preparation can be tedious and confusing, with hours of hands-on time and complicated multi-tube chemistries. SMARTer Apollo users can easily generate consistent, high-quality NGS libraries with complete SMARTer PrepX kits and compatible scripts. SMARTer PrepX kits provide every reagent necessary for library prep in prealiquoted, color-coded, single-use reagent strips. This makes deck setup simple: follow the prompts on the integrated touchscreen that tell you exactly where and how to place the reagents, minimizing error and stress.

SMARTer PrepX kit

Designed with flexibility in mind, SMARTer PrepX kits and compatible scripts accommodate a variety of sample throughputs and input amounts.

Cat. # SMARTer Apollo reagent kit Compatible script Script throughput Minimum input amount per sample
640101 SMARTer PrepX Complete ILMN DNA Library Kit, 24 Samples PrepX ILM 8 1–8 1 ng DNA
640102 SMARTer PrepX Complete ILMN 32i DNA Library Kit, 96 Samples PrepX ILM 32i 4–32 1 ng DNA
640096 SMARTer PrepX RNA-Seq for Illumina Library Kit, 24 Samples PrepX mRNA 8 1–8 100 pg polyA-enriched RNA; 2 ng rRNA-depleted mRNA
640097 SMARTer PrepX RNA-Seq for Illumina Library Kit, 48 Samples PrepX mRNA 48 6–48 100 pg polyA-enriched RNA; 2 ng rRNA-depleted mRNA
640098 SMARTer PrepX PolyA mRNA Isolation Kit, 96 Samples PrepX PolyA 8 or PrepX PolyA 48 1–8 or
100 ng total RNA
640099 SMARTer PrepX Small RNA for Illumina Library Kit, 24 Samples PrepX small RNA 8 1–8 100 ng total RNA
640100 SMARTer PrepX Small RNA for Illumina Library Kit, 48 Samples PrepX small RNA 48 6–48 100 ng total RNA

Set up the deck, hit run, and walk away

The SMARTer Apollo system’s graphic user interface (GUI) on the integrated touchscreen displays easy-to-follow instructions for SMARTer PrepX kit reagent placement. GUI-adapted protocols will display an overview of the deck setup and then call out each deck position to identify which plastic, what reagent, and how much of that reagent to load in a specific location. It also prompts you to add reagents and strips in a certain orientation, depending on the script and kit used.

SMARTer Apollo system′s integrated touchscreen that guides users through deck setup.

This screenshot is part of a series of images displayed on the SMARTer Apollo system’s integrated touchscreen that guides users through deck setup. Just verify the deck setup is correct, hit run, and the SMARTer Apollo system does the rest!

Please fill out the form for more information on how the Apollo system can optimize your NGS library prep for reliable sequencing results.

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