Takara Full transcriptome analysis of single cells with the SMART-Seq Stranded Kit

Get more out of your single-cell and ultra-low input RNA-seq with the SMART-Seq Stranded Kit. This kit uses a random-priming approach to capture the whole transcriptome, enabling analysis of nonpolyadenylated transcripts at the single-cell level. The kit contains reagents for generating stranded sequencing libraries, including cDNA synthesis and amplification, ZapR-mediated ribosomal RNA depletion, and Illumina-compatible library preparation.

If you prefer an oligo(dT) priming approach, we recommend our SMART-Seq HT Kit or SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

Overview

• Simple workflow to generate stranded Illumina sequencing-ready libraries in 7 hours
• Appropriate for analysis of 1–1,000 intact mammalian cells or 10 pg–10 ng of low- or high-quality mammalian total RNA
• Reproducible, accurate detection of full-length coding and noncoding transcripts from single cells or total RNA
• Comparable sensitivity to our gold-standard SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

Interested in more data and FAQs about this product? Visit the NGS Learning Center.

SMART-Seq Stranded Kit workflow

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Figure 1. Schematic of the SMART-Seq Stranded Kit workflow.

SMART-Seq Stranded Kit performs well across a wide range of inputs

Sequencing alignment metrics for A375 total RNA and cells
Input	Total RNA	1,000 cells	500 cells	100 cells	10 cells	5 cells	1 cell
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Number of reads (pairs)	6,000,000	6,000,000	6,000,000	6,000,000	6,000,000	6,000,000	5,873,974
Number of transcripts >1 FPKM	13,260	13,294	13,583	13,520	12,726	12,602	11,540
Number of transcripts >0.1 FPKM	21,334	21,113	21,365	21,145	20,550	18,888	15,815
Proportion of reads (%):
Exonic	34.7	36.4	39.2	42.7	36.7	36.2	37.3
Intronic	29.6	29.3	27.7	28.3	34.0	30.4	21.1
Intergenic	14.2	13.4	12.2	12.9	16.7	16.8	10.1
rRNA	7.0	11.4	11.5	6.3	3.6	4.9	7.1
Mitochondrial	4.1	3.5	3.7	4.9	3.8	4.4	4.6
Overall mapping (%)	89.6	93.9	94.3	95.1	94.9	92.7	80.2
Duplicate rate (%)	37.3	45.2	40.3	46.1	52.5	72.2	78.5
lncRNA mapping:
Number of mapped reads (%)	7.2	10.4	10.8	9.4	8.7	8.6	7.3
lncRNA transcripts detected	5,395	4,687	4,565	5,439	5,440	4,983	2,802

Figure 2: High reproducibility across cell input amounts. A375 cells isolated by FACS were used to generate RNA-seq libraries with the SMART-Seq Stranded Kit. Input varied from 1 cell to 1,000 cells, with two replicates per input of 5–1,000 cells and 12 replicates for the single cells. For comparison, two aliquots of 1,000 cells were used for total RNA purification and then used for library preparation.

SMART-Seq Stranded Kit matches the sensitivity of SMART-Seq v4 technology

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Figure 3. Comparison between SMART-Seq v4 and SMART-Seq Stranded kits. Single cells (K562) isolated by FACS were used to generate RNA-seq libraries with the SMART-Seq Stranded Kit (Stranded) and a SMART-Seq v4 Kit (SSv4; cDNA from this kit was further processed with a Nextera® XT DNA Library Preparation Kit). Panel A. The overlap in the total number of transcripts identified (FPKM >1) by each kit was analyzed and shown to be 83.8%. Panel B. *The number of transcripts identified (FPKM >1) in individual cells was similar between the two kits, with a tighter range across cells processed with the SSv4 kit. *Panel C. The reproducibility (Pearson correlation) of transcript expression levels across all cells from each kit was similar, although slightly higher and more consistent across cells processed with the Stranded kit.

More Information

Applications

• Generation of Illumina sequencing-ready libraries in 7 hours from small quantities of mammalian cells (1–1,000 cells) or total RNA (10 pg–10 ng)
• Whole transcriptome sequencing with strand-of-origin information

Additional product information

Please see the product`s Certificate of Analysis for information about storage conditions, product components, and technical specifications. Please see the Kit Components List to determine kit components. Certificates of Analysis and Kit Components Lists are located under the Documents tab.