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SMARTer NGS SMART-Seq Single Cell Kit technical note
Accurate detection of SNVs and CNVs from five-cell inputs in a single, low-pass sequencing run A single NGS assay for SNVs and CNVs
Guest webinar: automating the SMART-seq HT kit Guest webinar: automating the SMART-Seq HT Kit

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Alzheimer's disease research

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SMARTer NGS SMART-Seq Single Cell Kit technical note
Accurate detection of SNVs and CNVs from five-cell inputs in a single, low-pass sequencing run A single NGS assay for SNVs and CNVs
Guest webinar: automating the SMART-seq HT kit Guest webinar: automating the SMART-Seq HT Kit

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Single-cell analysis of Alzheimer's disease

In recent years, sequencing approaches have shed light on the genomic, epigenomic, and transcriptional dysregulation of Alzheimer's disease and other age-linked disorders. Genome-wide association studies have identified numerous risk loci (Kamboh et al. 2012; Jansen et al. 2019). RNA-seq reveals widespread transcriptomic dysregulation and altered splicing (Raj et al. 2018). Chromatin accessibility profiling demonstrates epigenomic changes in elderly and Alzheimer's-afflicted brains (Gjoneska et al. 2015; Klein et al. 2019).

However, brain tissue is extremely heterogeneous, and this represents an enormous research challenge due to the cellular basis of Alzheimer's disease: microglia and astrocytes promote inflammation, oligodendrocytes retract their protective myelin sheaths, neurons die and sever synaptic connections, and each of these pathologies is the result of unique disruptions in individual cell types. While a large proportion of sequencing work has been done using bulk tissue rather than single cells, breakthroughs in single-cell sequencing technologies have allowed researchers to begin examining the genomic, epigenomic, and transcriptional landscapes of individual cells. This has allowed the identification of Alzheimer's disease-associated cell types and revealed age- and Alzheimer's-linked genomic mosaicism (Bushman et al. 2015; Keren-Shaul et al. 2017; López-Sánchez et al. 2017).

By understanding the cellular basis of Alzheimer's disease, investigators will be more capable of monitoring and tailoring prophylactic and therapeutic interventions. Researchers have only begun to scratch the surface of what single-cell sequencing methods can tell us about this debilitating illness, but we know these approaches will require sensitive, reproducible, and high-throughput methods.

Fortunately, we're up to the task.

Highlighted products

Ultra-sensitive single-cell sequencing

Our new SMART-Seq Single Cell Kit (SSsc) incorporates our proprietary SMART (Switching Mechanism at 5' end of RNA Template) technology to offer unprecedented sensitivity from intact single cells or nuclei. It offers greater sensitivity and reproducibility than Smart-Seq2 with a reduced percentage of dropouts (Figure 1). Indeed, its optimized chemistry outperforms all currently available full-length sequencing methods for single-cell applications, including our gold-standard SMART-Seq v4 technology (Figure 2), which currently powers the transcriptomic arm of the Allen Cell Types Database. These features make SSsc the ideal chemistry specifically for single-cell applications and an optimal choice for characterizing the transcriptional diversity of the CNS. Additional benefits include its compatibility with automation platforms and a user-friendly, plate-based workflow. Finally, for high-throughput workflows, we offer both our automation-friendly SMART-Seq HT Kit and our ICELL8 cx Single-Cell System—an advanced automation platform for single-cell sequencing workflows (more in the next section, below).

SMART-Seq Single Cell Kit outperforms Smart-seq2

Figure 1. The SMART-Seq Single Cell Kit outperforms the Smart-seq2 protocol. Single cells from the lymphoblastoid cell line GM12878 were processed with SSsc (18 cells) or Smart-seq2 (20 cells) using 19 cycles of PCR. As described in the methods, RNA-seq libraries were generated and sequences analyzed (after normalizing all samples to 1.75 million paired-end reads). Panel A. The read distribution varied between the two chemistries, with increased mitochondrial reads using Smart-seq2 and increased exonic reads using SSsc. Panel B. More genes were detected in the cells processed with SSsc. Panel C. Correlation boxplots showing the intragroup Spearman correlation between all cells processed with either method. The higher Spearman correlation among the cells processed with SSsc indicates a greater reproducibility than the Smart-seq2 method. Panel D. The greater reproducibility of SSsc is also demonstrated by the lower dropout rate of the genes detected with a TPM >1.

Our optimized SMART-Seq Single Cell chemistry outperforms the former gold-standard SMART-Seq v4

Figure 2. Improved performance for single cells with low RNA content. 12 single cells from lymphoblastoid cell line GM22601 were processed with SMART-Seq v4 (SSv4) or SSsc using 19 cycles of PCR. As described in the methods, RNA-seq libraries were generated and sequences analyzed (after normalizing all samples to 1.25 million paired-end reads). Panel A. The cDNA yield generated with SSsc is drastically higher than that generated with SSv4. Panel B. The read distribution was fairly similar between the two chemistries. Panel C. Over 50% more genes were detected in the cells processed with SSsc. Panel D. Correlation boxplots showing intragroup Spearman correlation between all cells processed with either method. The higher Spearman correlation among the cells processed with SSsc indicates a greater reproducibility than SSv4.

In addition to single-cell RNA-seq methods, we also offer best-in-class DNA-seq solutions in the form of our PicoPLEX WGA and PicoPLEX Gold single-cell DNA-seq kits. These kits use our high-performance PicoPLEX technology for single-cell whole genome amplification, employing multiple cycles of quasi-random priming followed by amplification with high-fidelity DNA polymerases to achieve superior performance than MDA-based methodologies. This allows for unbiased and accurate amplification of the genome, enabling the sensitive, reproducible, and accurate genomic coverage needed for identifying single-nucleotide variants (SNVs), copy-number variants (CNVs), insertions, and deletions (Figure 3). Indeed, researchers have cited the use of our PicoPLEX technology to reveal age-linked mosaic CNVs in human brain (Chronister et al. 2019) and neuronal tetraploidy associated with reduced cognition in an animal model of AD (López-Sánchez et al. 2017).

Detection of CNVs in two individual cells with SMARTer PicoPLEX Gold Single Cell DNA-seq Kit

Figure 3. CNVs detected in two individual cells using the PicoPLEX Gold Single Cell DNA-seq Kit. Log2 ratio of the total number of reads in 50-kb bins from single NCI-H929 cells, shown as one cell in Panel A and a second cell in Panel B. Red bars represent copy-number gains while blue bars represent losses. The top row of the graphs in each panel depicts the control bulk sample sequenced to a depth of 90 million read pairs. The highly reproducible coverage of the PicoPLEX Gold kit enables the accurate detection of structural variants as small as 100 kb, even at shallow sequencing depths (2.5–8.5 million read pairs).

Automated, high-throughput single-cell sequencing solutions

Our ICELL8 cx Single-Cell System is an open, high-throughput platform that provides an end-to-end solution for isolating, imaging, and generating libraries from single cells. Cells are stained, dispensed into a 5,184-nanowell chip at an average of one cell per well, and imaged. The images are analyzed by the integrated cell selection software, which automatically identifies and processes only nanowells containing single cells to eliminate noise from empty and multiplet-containing nanowells (Figure 4). Targeted nanowells are then processed on-chip, with minimal hands-on time, to generate cDNA or sequencing libraries according to your desired workflow. Many publications have cited the use of our ICELL8 technology to power their high-throughput scRNA-seq analyses, including its usage to transcriptomically profile single nuclei from human cortical and retinal tissue (Hochgerner et al. 2017; Liang et al. 2018).

The ICELL8 cx Single-Cell System's integrated CellSelect software automatically selects single, live cells for processing.

Figure 4. The ICELL8 cx Single-Cell System's integrated CellSelect Software automatically selects only single, live cells for processing. Following imaging of the ICELL8 chip, all 5,184 nanowells are automatically screened for downstream processing. Empty wells and wells containing multiple cells are rejected (Panel B) while only cells containing single cells (Panel A) are selected and processed, minimizing background noise and ensuring true single cell libraries.

We offer preprinted chips and reagents for several prevalidated NGS applications, including differential expression by 3'-end counting; full-length scRNA-seq for improved detection of SNPs, fusions, and alternative splice variants; and TCR profiling/5'-end differential expression. The greatest strength of our ICELL8 system, however, is its flexibility: researchers have taken advantage of this open platform to develop high-throughput, single-cell workflows for scRNA-seq of intact adult cardiomyocytes, single-cell ATAC-seq, CUT&Tag, and pheno-seq (Yekelchyk et al. 2019; Mezger et al. 2018; Tirier et al. 2018; Kaya-Okur et al. 2019).

We invite you to learn more about the solutions we offer for improving your sequencing workflows. Please reach out to us with any questions or requests and to schedule a trial of this technology via the "contact us" form on the left. If you are on a mobile device, click on the hamburger icon () on the top left of your screen, then scroll down to access the registration form.


References for AD genetic analysis studies

Bushman, D. M. et al. Genomic mosaicism with increased amyloid precursor protein (APP) gene copy number in single neurons from sporadic Alzheimer's disease brains. eLife 4, (2015).

Gjoneska, E. et al. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature 518, 365–369 (2015).

Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk. Nat. Genet. 51, 404–413 (2019).

Kamboh, M. I. et al. Genome-wide association study of Alzheimer's disease. Transl. Psychiatry 2, e117 (2012).

Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer's disease. Cell 169, 1276–1290.e17 (2017).

Klein, H.-U. et al. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. Nat. Neurosci. 22, 37–46 (2019).

López-Sánchez, N. et al. Neuronal tetraploidization in the cerebral cortex correlates with reduced cognition in mice and precedes and recapitulates Alzheimer's-associated neuropathology. Neurobiol. Aging 56, 50–66 (2017).

Raj, T. et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility. Nat. Genet. 50, 1584–1592 (2018).

References citing the use of our SMART-Seq kits for scRNA-seq, PicoPLEX kits for scDNA-seq, and ICELL8 technology in CNS and Alzheimer's disease research

Chronister, W. D. et al. Neurons with complex karyotypes are rare in aged human neocortex. Cell Rep. 26, 825–835.e7 (2019).

Hochgerner, H. et al. STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array. Sci. Rep. 7, 16327 (2017).

Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. bioRxiv 568915 (2019). doi:10.1101/568915

Liang, Q. et al. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling. bioRxiv 468207 (2018). doi:10.1101/468207

López-Sánchez, N. et al. Neuronal tetraploidization in the cerebral cortex correlates with reduced cognition in mice and precedes and recapitulates Alzheimer's-associated neuropathology. Neurobiol. Aging 56, 50–66 (2017).

Mezger, A. et al. High-throughput chromatin accessibility profiling at single-cell resolution. Nat. Commun. 9, 3647 (2018).

Tirier, S. M. et al. pheno-seq—linking 3D phenotypes of clonal tumor spheroids to gene expression. bioRxiv 311472 (2018). doi:10.1101/311472

Yekelchyk, M. et al. Mono- and multi-nucleated ventricular cardiomyocytes constitute a transcriptionally homogenous cell population. Basic Res. Cardiol. 114, 36 (2019)


Mapping the brain, one cell type at a time

Single-cell transcriptomics has provided a powerful new way to identify and characterize the various cell types that comprise complex tissues and organs. In this video, Dr. Bosiljka Tasic (Allen Institute for Brain Science) discusses a method she and her team developed to investigate the most complex organ of all: the mammalian brain.

Blog: how the Allen Institute developed a workflow for generating transcriptional data from single brain-cell nuclei


Featured products

Cat. # Product Size License Quantity Details
634437 SMART-Seq® HT Kit 96 Rxns USD $2671.00

License Statement

ID Number  
275 SMART-Seq2 Technology. This product is sold under exclusive license from Ludwig Institute of Cancer Research, Ltd. and is covered by US Patent No. 10266894, Japanese Patent No. 6336080, and European Patent No. 3036336, and pending U.S. patent application and/or pending claims of foreign counterparts. For license information, please contact a Takara Bio USA, Inc. licensing representative by phone at 650.919.7320 or by e-mail at licensing@takarabio.com.
388 This product is protected by Canadian Patent No. 2921603 and Japanese Patent Nos. 6336080 and 6603699 and corresponding US and foreign pending patents. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.

The SMART-Seq HT Kit is an automation-friendly kit designed for the synthesis of high-quality cDNA directly from 1–100 intact cells or ultra-low amounts of total RNA (10–1,000 pg). cDNA libraries generated with this kit have been tested for compatibility with Illumina sequencing platforms. This kit supports up to 96 reactions.

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Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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Gene expression data obtained from FACS-sorted 293T cells

Gene expression data obtained from FACS-sorted 293T cells

High reproducibility of gene expression data obtained from FACS-sorted 293T cells using the SMART-seq v4 and SMART-Seq HT kits. Libraries generated from twenty-one individual 293T cells (table, top panel) were further analyzed to evaluate the reproducibility of gene expression measurements obtained for each cell with the SMART-Seq v4 kit (SSv4_1 to SSv4_12) and the SMART-Seq HT Kit (HT_1 to HT_9)(lower panel). The hierarchical clustering heat map shows Euclidean distances between all the cells and reports Pearson correlations ranging from 0.74 to 0.97. While the best correlations are observed between cells prepared with one or the other kit, the correlations are still very high between the two kits and the cells are not clustering based on the library preparation method. These data demonstrate that the modified workflow in the SMART-Seq HT Kit does not introduce major bias in measurement of gene expression levels.

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Comparison of expression level by gene GC content between the SMART-Seq v4 and SMART-Seq HT kits

Comparison of expression level by gene GC content between the SMART-Seq v4 and SMART-Seq HT kits

Comparison of expression level by gene GC content between the SMART-Seq v4 and SMART-Seq HT kits. The libraries made from 10 pg of Mouse Brain Total RNA shown in the table (Figure 2) were further analyzed for GC content representation (see table, top panel). Genes were binned by GC content, and correlation plots were used to visualize the reproducibility of the expression levels (FPKM) of genes in each bin. The average gene counts are very reproducible for replicate samples analyzed using the SMART-Seq v4 (Panel A) or SMART-Seq HT kits (Panel B). Genes with high or low GC content (shown in red and blue, respectively) show similar expression levels in the SMART-Seq v4 and SMART-Seq HT kits (Panel C). Thus, the One-Step RT PCR reaction introduced in the new SMART-seq HT Kit maintains the representation of the low- and high-GC content genes.

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High overlap of transcripts identified with the SMART-Seq v4 and SMART-Seq HT kits

High overlap of transcripts identified with the SMART-Seq v4 and SMART-Seq HT kits

High overlap of transcripts identified with the SMART-Seq v4 and SMART-Seq HT kits. Libraries prepared from 10 pg of Mouse Brain Total RNA shown in Table 1 were further evaluated for the overlap in the number of transcripts identified (FPKM >0.1) between technical replicates within each kit, and found to be very similar (61–63% overlap) (Panel A). Transcripts identified by all three replicates for each kit were then compared against each other, indicating an overlap of 71%. The overlapping transcripts have an average expression level of 37 FPKM, while the transcripts uniquely identified with individual kits are less abundant, averaging between 6–7 FPKM, indicating that the transcripts more likely to not be identified are the ones expressed at a low level.

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Schematic of technology in the SMART-Seq HT Kit

Schematic of technology in the SMART-Seq HT Kit

Schematic of technology in the SMART-Seq HT Kit. SMART technology is used in a ligation-free workflow to generate full-length cDNA. The reverse transcriptase (RT) adds non-templated nucleotides (indicated by Xs) which hybridize to the SMART-Seq HT Oligonucleotide, providing a new template for the RT. Chemical modifications to block ligation during sequencing library preparation are present on some primers (indicated by black stars). The SMART adapters, added by the oligo (dT) primer (SMART-Seq CDS Primer IIA) and SMART-Seq HT Oligonucleotide and used for amplification during PCR, are indicated in green. The one-step RT-PCR is set up as a single reaction so that all the reagents are mixed together but then used sequentially. SeqAmp polymerase is a hot-start DNA polymerase and is activated only after the reverse transcription/template-switching step is complete.

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Comparison of the SMART-Seq v4 and SMART-Seq HT kit workflows

Comparison of the SMART-Seq v4 and SMART-Seq HT kit workflows

Comparison of the SMART-Seq v4 and SMART-Seq HT kit workflows. The SMART-Seq v4 method (left) was modified to generate a simplified, high-throughput workflow (SMART-Seq HT, right) with very little hands-on time. Once single cells have been obtained using FACS, the SMART-Seq HT Kit involves only three hands-on steps, while the original SMART-Seq v4 kit involves six hands-on steps. One key step in the SMART-Seq HT workflow is the One-Step RT-PCR, performed using the One-Step RT-PCR Buffer, formulated specifically for optimal reverse transcription followed by efficient PCR cDNA amplification. The One-Step RT-PCR Buffer is directly compatible with AMPure bead purification without the need for addition of Lysis Buffer. As with the original SMART-Seq v4 kit, the SMART-Seq HT Kit requires validation (quantification and assessment of high molecular weight, full-length cDNA) before cDNA is used for sequencing library preparation (Nextera XT).

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634437: SMART-Seq HT Kit

634437: SMART-Seq HT Kit
R300718 PicoPLEX® Single Cell WGA Kit v3 24 Rxns USD $590.00

License Statement

ID Number  
M54 This product is covered by the claims of U.S. Patent Nos. 7,704,713 and its foreign counterparts. 

The PicoPLEX Single Cell WGA Kit v3 uses a single-tube protocol developed specifically for the reproducible amplification of genomic DNA (gDNA) starting from 1–10 cells or equivalent picogram quantities of isolated gDNA. Cell lysis and whole-genome preamplification are followed by high-fidelity amplification with very low background to yield over 2 µg of product in under 3 hours. This kit is suited for applications in which base-level resolution is required, such as for the detection of mutations. This product contains reagents for 24 reactions.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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R300718: PicoPLEX Single Cell WGA Kit v3

R300718: PicoPLEX Single Cell WGA Kit v3
R300669 PicoPLEX® Gold Single Cell DNA-seq Kit 24 Rxns USD $1080.00

License Statement

ID Number  
325 Patent pending. For further information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
M54 This product is covered by the claims of U.S. Patent Nos. 7,704,713 and its foreign counterparts. 
328 This product is protected by U.S. Patents 8,206,913 and corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.

The PicoPLEX Gold Single Cell DNA-Seq Kit is designed to generate high-quality DNA libraries from single cells for sequencing on Illumina platforms. The kit is based on innovative PicoPLEX technology and yields libraries with superior reproducibility from 1–5 mammalian cells or genome equivalents of gDNA as input, providing reliable results from challenging samples such as formalin-fixed single cells. Single index, dual index, and unique dual index kits are available and must be purchased separately. This product contains reagents for 24 reactions.

The kit features a streamlined workflow consisting of four steps—from input to amplified NGS libraries—that can be completed in less than four hours. The kit uses high-fidelity enzymes and optimized primers and is suitable for accurate and reproducible profiling of copy number variants (CNVs), single-nucleotide variants (SNVs), indels, and other small structural variants. The kit is compatible with single cells and purified DNA from humans, animals, and bacteria, as well as single flow-sorted chromosomes.

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Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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SMARTer PicoPLEX Gold Single Cell DNA-Seq technology: a four-step reaction that starts with a single cell

SMARTer PicoPLEX Gold Single Cell DNA-Seq technology: a four-step reaction that starts with a single cell

SMARTer PicoPLEX Gold Single Cell DNA-Seq technology: a four-step reaction that starts with a single cell. Cellular gDNA extracted in Step 1 is used as template for multiple cycles of quasi-random priming and linear amplification followed by exponential library amplification.

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SMARTer PicoPLEX Gold Single Cell DNA-Seq Kit workflow

SMARTer PicoPLEX Gold Single Cell DNA-Seq Kit workflow

SMARTer PicoPLEX Gold Single Cell DNA-Seq Kit workflow. The four-step SMARTer PicoPLEX Gold Single Cell DNA-Seq workflow takes place in two tubes or plates and is completed in less than 3 hours with just 30 minutes of hands-on time.

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R300669: PicoPLEX Gold Single Cell DNA-seq Kit

R300669: PicoPLEX Gold Single Cell DNA-seq Kit
640188 ICELL8® cx Single-Cell System Each Inquire for Quotation

License Statement

ID Number  
329 This product is protected by one or more of these U.S. Patents 9,132,427, 9,909,171, 9,447,925, 9,951,381 and/or corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
397 This product is protected by U.S. Pat. No. 11,460,405 and corresponding foreign patents pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
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The ICELL8 Single-Cell System is an advanced, integrated automation platform that combines the power of imaging and dispensing with the isolation of single cells in 5,184-nanowell chips. This open-platform, high-throughput system is prevalidated for use with several NGS applications, and also provides the flexibility to enable users to develop applications of their choice.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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640188: ICELL8 cx Single-Cell System

640188: ICELL8 cx Single-Cell System
634472 SMART-Seq® Single Cell Kit 96 Rxns USD $5367.00

License Statement

ID Number  
275 SMART-Seq2 Technology. This product is sold under exclusive license from Ludwig Institute of Cancer Research, Ltd. and is covered by US Patent No. 10266894, Japanese Patent No. 6336080, and European Patent No. 3036336, and pending U.S. patent application and/or pending claims of foreign counterparts. For license information, please contact a Takara Bio USA, Inc. licensing representative by phone at 650.919.7320 or by e-mail at licensing@takarabio.com.

The SMART-Seq Single Cell Kit is designed to generate high-quality, full-length cDNA directly from single cells. It has been validated with 2 pg of total RNA input and with single cells known to have low RNA content (e.g., peripheral blood mononuclear cells). This kit supports up to 96 reactions.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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634472: SMART-Seq Single Cell Kit

634472: SMART-Seq Single Cell Kit

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The SMART-Seq Single Cell PLUS Kit demonstrates greater discrimination between control and single-cell samples than NEBNext.

The SMART-Seq Single Cell PLUS Kit demonstrates greater discrimination between control and single-cell samples than NEBNext.

Clustering of the SSsc single cell and positive controls and significantly distinct discrimination of the negative controls provides confidence in the data generated with SSsc PLUS. By UMAP analysis, there is a clear separation between the negative controls and the positive controls/single-cell samples for SSsc PLUS. As expected, the positive controls (grey) and the single-cell samples (green) cluster together for the SSsc PLUS while the negative controls (dusty blue) cluster together near the bottom of the chart. Interestingly, the SSsc PLUS negative controls and all of the NEBNext samples cluster together: negative (red), positive (light blue), and the single cells (purple). These analyses indicate that experimental noise, even when working with such small amounts of starting material, will not affect confidence in the biological import of the results.

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Automation and miniaturization of SSsc on the mosquito HV.

Automation and miniaturization of SSsc on the mosquito HV.

Comparing full-volume versus eighth-volume processing on the mosquito HV with single CHO cells. Boxplots of gene counts for each preparation (medians: FV=16,592, Eighth=16,014). Boxplots show similar sensitivity for FV versus miniaturized volumes. All boxplots interquartile range (IQR) is the 25th and 75th quartiles; the whiskers are 1.5X IQR from the median value and represent the extremes of the data

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Automation and miniaturization of SSsc on the MANTIS liquid handler.

Automation and miniaturization of SSsc on the MANTIS liquid handler.

Comparing full-volume versus quarter-volume processing with single GM12878 cells on the MANTIS liquid handler. Boxplots of gene counts for each preparation (medians: FV=9,980, Quarter=9,603). Boxplots show similar sensitivity for FV versus miniaturized volumes. All boxplots interquartile range (IQR) is the 25th and 75th quartiles; the whiskers are 1.5X IQR from the median value and represent the extremes of the data.

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Performance comparison of SS2 versus SSsc with GM12878 cells and SS3 versus SSsc with primary T cells isolated from PBMCs.

Performance comparison of SS2 versus SSsc with GM12878 cells and SS3 versus SSsc with primary T cells isolated from PBMCs.

Boxplots representing the distribution of gene counts for TPM > 0.1. The boxes denote the interquartile range (IQR), i.e., the 25th and 75th quartiles; the whiskers are 1.5X IQR from the median value and represent the extremes of the data. Outliers are plotted as empty circles.

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Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, TBUSA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

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Explore what makes good science possible

Mapping the brain, one cell type at a time

Single-cell transcriptomics has provided a powerful new way to identify and characterize the various cell types that comprise complex tissues and organs. In this video, Dr. Bosiljka Tasic (Allen Institute for Brain Science) discusses a method she and her team developed to investigate the most complex organ of all: the mammalian brain.

Blog: how the Allen Institute developed a workflow for generating transcriptional data from single brain-cell nuclei

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Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, TBUSA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

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