SMART-Seq Single Cell Kit
SMART-Seq Single Cell Kit
Brand: Takara Bio.
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SMART-Seq Single Cell Kit
SMART-Seq Single Cell Kit—full-length transcriptome analysis with ultimate sensitivity for single cells
The SMART-Seq Single Cell Kit (SSsc) is powered by robust chemistry that provides unparalleled sensitivity and reproducibility for single-cell and nuclei applications. This kit uses oligo(dT) priming to generate high-quality, full-length cDNA directly from single cells known to have low RNA content (e.g., PBMCs, T-cells, B-cells, etc.).
The SMART (Switching Mechanism at 5' End of RNA Template) technology powering the SMART-Seq Single Cell kit provides full-length transcript information, enabling analysis of transcript isoforms, gene fusions, point mutations, etc. The cDNA kit provides high reproducibility, even gene-body coverage, and an accurate representation of GC-rich transcripts. We have further modified this powerful core technology to create a new chemistry with higher sensitivity designed specifically for single-cell applications. These enhancements result in more useful reads and a higher gene detection, allowing for a better understanding of precious samples.
The SSsc PLUS kit includes our patented library preparation kit that incorporates enzymatic fragmentation and stem-loop adapters to construct high-quality, Illumina-compatible libraries from the cDNA synthesized with the core kit. This two-step workflow takes place in a single tube and can be completed in about two hours with no intermediate purification steps necessary—minimizing sample mix-up, sample loss, and cross-contamination. The high library yield generated from this kit provides the flexibility to sequence on high-throughput sequencers while providing high reproducibility.
If you are interested in these benefits but are working with intact, high-quality cells (<1,000) or ultra-low total RNA inputs, we recommend our SMART-Seq v4 Kit.
If you prefer a random priming approach that will allow you to work with degraded samples and includes library preparation and indexing reagents, we recommend our SMART-Seq Stranded Kit.
Overview
- Easy, plate-based workflow—direct input of single cells isolated by FACS or other methods
- Unparalleled sensitivity and reproducibility—get the best performance for single-cell RNA-seq (especially for cells with very low RNA content and for nuclei) with the highest gene detection
- Robust, full-length chemistry—outperform all existing single-cell full-length methods, including Smart-seq2, with this validated protocol
- Increased sequencing power—include unique dual indexes to allow for the pooling of multiple samples and confident sequencing on the NovaSeq™ system
- Highly scalable workflow—automate and use for high-throughput applications
Applications
- cDNA synthesis from single cells for full-length transcriptome sequencing
- cDNA outputs from the SSsc kit can be used with the SMART-Seq Library Prep kit (not sold separately; sold as part of the SSsc PLUS kit) for Illumina sequencing
SMART-Seq Single Cell Kit provides higher sensitivity than Smart-seq2
Validated kit backed by expert technical support
The SMART-Seq Single Cell Kit outperforms Smart-seq2. Single cells from the lymphoblastoid cell line GM12878 were processed with the SMART-Seq Single Cell Kit (SSsc; 18 cells) or the Smart-seq2 method (Smart-seq2; 20 cells) using 19 cycles of PCR. RNA-seq libraries were generated and sequences analyzed (after normalizing all samples to 1.75 million paired-end reads). Panel A. The read distribution was different between the two chemistries, with a drastically higher number of reads mapping to the mitochondrial genome (and therefore, fewer reads available for gene identification) with Smart-seq2 chemistry. Panel B. More genes were detected in the cells processed with SSsc. For additional data on reproducibility and sensitivity, view our technical note.
Even higher sensitivity for single-cell applications
We have further modified our core technology to create a new chemistry with higher sensitivity designed specifically for single-cell applications. We demonstrated that the new SSsc kit generates data with even better sensitivity and reproducibility than the SMART-Seq v4 kit (SSv4).
The SMART-Seq Single Cell Kit's improved chemistry is highly suitable for single-cell applications. Panel A. 12 single cells from lymphoblastoid cell line GM22601 were processed with SSv4 or SSsc using 19 cycles of PCR. All samples were normalized to 1.25 million paired-end reads. The cDNA yield generated with SSsc was drastically higher than that generated with SSv4. Panel B. About 50 single PBMCs from one donor were processed with SSv4 or SSsc. About 60% more genes were detected in the cells processed with SSsc, regardless of the number of reads used for the analysis.
SSsc outperforms the NEBNext single-cell protocol
The SMART-Seq Single Cell Kit outperforms the NEBNext protocol. Libraries were prepared from T cells according to manufacturer's instructions with either SSsc or NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina. Panel A. In these boxplots, the box denotes the interquartile range (IQR), i.e., the 25th and 75th quartiles; the whiskers are 1.5 x IQR from the median value and represent the extremes of the data. The number of genes identified with a TPM >0.1 is higher (~40%) for SSsc (median = 3,591) than for NEBNext (median = 2,665). Panel B. The read distribution is different between the two chemistries, with more reads mapping to exon regions for SSsc. Panel C. The high number of cycles required to generate a library for the NEBNext protocol means that the negative controls for NEB (red) cluster strongly with the single-cell libraries (light blue), while the negative controls for SSsc (purple) are distinct from the single-cell libraries (dark blue).
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SMART-Seq Single Cell Kit provides higher sensitivity than Smart-seq2
Validated kit backed by expert technical support
The SMART-Seq Single Cell Kit outperforms Smart-seq2. Single cells from the lymphoblastoid cell line GM12878 were processed with the SMART-Seq Single Cell Kit (SSsc; 18 cells) or the Smart-seq2 method (Smart-seq2; 20 cells) using 19 cycles of PCR. RNA-seq libraries were generated and sequences analyzed (after normalizing all samples to 1.75 million paired-end reads). Panel A. The read distribution was different between the two chemistries, with a drastically higher number of reads mapping to the mitochondrial genome (and therefore, fewer reads available for gene identification) with Smart-seq2 chemistry. Panel B. More genes were detected in the cells processed with SSsc. For additional data on reproducibility and sensitivity, view our technical note.
Even higher sensitivity for single-cell applications
We have further modified our core technology to create a new chemistry with higher sensitivity designed specifically for single-cell applications. We demonstrated that the new SSsc kit generates data with even better sensitivity and reproducibility than the SMART-Seq v4 kit (SSv4).
The SMART-Seq Single Cell Kit's improved chemistry is highly suitable for single-cell applications. Panel A. 12 single cells from lymphoblastoid cell line GM22601 were processed with SSv4 or SSsc using 19 cycles of PCR. All samples were normalized to 1.25 million paired-end reads. The cDNA yield generated with SSsc was drastically higher than that generated with SSv4. Panel B. About 50 single PBMCs from one donor were processed with SSv4 or SSsc. About 60% more genes were detected in the cells processed with SSsc, regardless of the number of reads used for the analysis.
SSsc outperforms the NEBNext single-cell protocol
The SMART-Seq Single Cell Kit outperforms the NEBNext protocol. Libraries were prepared from T cells according to manufacturer's instructions with either SSsc or NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina. Panel A. In these boxplots, the box denotes the interquartile range (IQR), i.e., the 25th and 75th quartiles; the whiskers are 1.5 x IQR from the median value and represent the extremes of the data. The number of genes identified with a TPM >0.1 is higher (~40%) for SSsc (median = 3,591) than for NEBNext (median = 2,665). Panel B. The read distribution is different between the two chemistries, with more reads mapping to exon regions for SSsc. Panel C. The high number of cycles required to generate a library for the NEBNext protocol means that the negative controls for NEB (red) cluster strongly with the single-cell libraries (light blue), while the negative controls for SSsc (purple) are distinct from the single-cell libraries (dark blue).
