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Technical notes View data for this product
Technical notes View data for FFPE samples
Home › Learning centers › Next-generation sequencing › Technology and application overviews › Biomarker discovery with RNA-seq

Next-generation sequencing

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    • Single-cell RNA- and DNA-seq
      • All-in-one cDNA synthesis and library prep from single cells
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      • Stranded libraries from single cells
      • Streamlined single-cell mRNA-seq
      • Full-length mRNA libraries from single cells (SMART-Seq v4)
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      • Next-gen WGA method for CNV and SNV detection from single cells
    • RNA-seq
      • Stranded libraries from picogram-input total RNA (v3)
      • Automation-friendly, all-in-one cDNA synthesis and library prep
      • All-in-one cDNA synthesis and library prep from ultra-low RNA inputs
      • Stranded libraries from picogram-input total RNA (v2)
      • Stranded libraries from FFPE inputs (v2)
      • Stranded libraries from 100 ng - 1 ug total RNA
      • Stranded libraries from 100 pg-100 ng total RNA
      • Stranded libraries from picogram-input total RNA (v1)
      • Stranded RNA-seq competitor kit comparison
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      • Sensitive capture of full-length transcript information with targeted RNA-seq
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      • Comparing ThruPLEX HV PLUS to Kapa and NEBNext
      • Improvements to ThruPLEX HV
      • ThruPLEX HV outperforms NEBNext Ultra II
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      • Tag-seq variant detection
      • Low-volume DNA shearing for SMARTer ThruPLEX library prep
    • Immune profiling
      • BCR repertoire profiling from human samples (bulk)
      • Improved TCR repertoire profiling from human samples (bulk)
      • TCR repertoire profiling from human samples (single cells)
      • TCR repertoire profiling from human samples (bulk)
      • TCR repertoire profiling from mouse samples (bulk)
      • BCR repertoire profiling from mouse samples (bulk)
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Technical notes View data for this product
Technical notes View data for FFPE samples

Discover more RNA biomarkers with Pico v2 RNA-seq

RNA-seq is an important tool for uncovering biomarkers that can be important in understanding the onset or progression of a disease, such as cancer. SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input (Pico v2) from Takara Bio has unrivaled sensitivity that can help researchers extract these biomarkers from a broad range of sample types, including FFPE RNA, cell-free RNA, and extracellular vesicles.

  • Unmatched sensitivity to find and uncover relevant biomarkers
  • Robust performance with challenging FFPE and cell-free RNA samples
  • Random-priming approach to detect coding and noncoding transcripts
  • Built-in patented rRNA depletion technology
  • Up to 384 unique dual indexes for use on the NovaSeq™ system

Coding and noncoding transcript production from DNA

Detect coding and noncoding transcripts with high sensitivity

With the Pico v2 kit, short, overlapping reads originating from the different strands of genomic DNA can be distinguished, enabling more accurate detection of noncoding RNAs that can overlap coding regions and often may not have polyadenylation. Thus, in addition to accurate and sensitive detection of mRNAs, this kit can also detect lncRNAs, tRNAs, and snoRNAs. More information »


NGS of FFPE samples

Get high-quality data from degraded FFPE samples

Obtaining good-quality sequencing data from FFPE samples can be a challenge since FFPE RNA integrity can range from high quality to highly degraded. The Pico v2 kit enables good representation of desirable RNA types in a single sequencing experiment, allowing researchers to detect a broad range of different biomarkers from both coding and noncoding RNAs. Get the most out of FFPE RNA with SMARTer chemistry. More information »


RNA-seq in human biofluids

Accurately detect RNA transcripts from extracellular vesicles

In a landmark study, researchers from the Center for Medical Genetics at Ghent University and Biogazelle, Zwijnaarde (Belgium) assessed the performance of the Pico v2 kit for RNA-seq analysis of the contents of extracellular vesicles derived from different biofluids. In this extensive assessment, they demonstrated that the kit provided an accurate, precise, and sensitive method to quantify total RNA in human biofluids. More information »


ZapR role in the SMARTer Stranded Pico v2 workflow

Remove unwanted transcripts with ZapR

Numerous strategies are available to avoid wasting reads on unwanted transcripts, like rRNA, when doing RNA-seq. Unfortunately, most are very sample-hungry and are ineffective on small quantities of RNA or on degraded RNA. The Pico v2 kit includes a fully integrated method for removal of unwanted transcripts at the cDNA level—so you don't need to go through costly, time-consuming depletion steps and lose your precious RNA before you even get started with library prep. More information »


SMARTer RNA-seq

Use unique dual indexes to mitigate index hopping on the NovaSeq system

In order to capitalize on the low cost per sample on the NovaSeq system, experimental design is critical, down to the type of indexes used for sample multiplexing. Unique dual indexes (UDIs) are a requirement to mitigate "index hopping" that can lead to read misassignment on the NovaSeq system. Take the best care of your hard-earned reads using SMARTer unique dual indexes for high-throughput sequencing. More information »


Related products (visit takarabio.com/picov2 for additional configurations)

Cat. # Product Size Price License Quantity Details
634411 SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian 12 Rxns USD $1054.00

License Statement

ID Number  
391 LIMITED USE LABEL LICENSE: RESEARCH USE ONLY Notice to Purchaser: This product is subject to a license granted to Takara Bio USA, Inc. and its Affiliates from Caribou Biosciences, Inc., and this product is transferred to the end-user purchaser (“Purchaser”) subject to a “Limited Use Label License” conveying to the Purchaser a limited, non-transferable right to use the product, solely as provided to Purchaser, together with (i) progeny or derivatives of the product generated by the Purchaser (including but not limited to cells), and (ii) biological material extracted or derived from the product or its corresponding progeny or derivatives (including but not limited to cells) (collectively, the product, and (i) and (ii) are referred to as “Material”) only to perform internal research for the sole benefit of the Purchaser. The Purchaser cannot sell or otherwise transfer Material to a third party or otherwise use the Material for any Excluded Use. “Excluded Use” means any and all: (a) commercial activity including, but not limited to, any use in manufacturing (including but not limited to cell line development for purposes of bioproduction), product testing, or quality control; (b) preclinical or clinical testing or other activity directed toward the submission of data to the U.S. Food and Drug Administration, or any other regulatory agency in any country or jurisdiction where the active agent in such studies comprises the Material; (c) use to provide a service, information, or data to a third party; (d) use for human or animal therapeutic, diagnostic, or prophylactic purposes or as a product for therapeutics, diagnostics, or prophylaxis; (e) activity in an agricultural field trial or any activity directed toward the submission of data to the U.S. Department of Agriculture or any other agriculture regulatory agency; (f) high throughput screening drug discovery purposes (i.e., the screening of more than 10,000 experiments per day) as well as scale-up production activities for commercialization; (g) modification of human germline, including editing of human embryo genomes (with the sole exception of editing human embryonic stem (ES) cell lines for research purposes) or reproductive cells; (h) self-editing; and/or (i) stimulation of biased inheritance of a particular gene or trait or set of genes or traits (“gene drive”). It is the Purchaser’s responsibility to use the Material in accordance with all applicable laws and regulations. For information on obtaining additional rights, including commercial rights, please contact licensing@cariboubio.com or Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA 94710 USA, Attn: Licensing.
395 This product is protected by U.S. Patent No. 10150985 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 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian is used to generate strand-specific RNA-seq libraries for Illumina sequencing from 250 pg–10 ng inputs of purified total RNA. This kit incorporates Takara Bio’s proprietary SMART (Switching Mechanism at the 5’ end of RNA Template) technology and includes refinements to the SMARTer method for stranded RNA-seq that simplify the library preparation workflow and improve sequencing performance. This method was developed to work with either high- or low-quality total RNA, does not require additional rRNA removal methods or kits, and produces sequencing libraries that retain strand-of-origin information. The integrated removal of cDNAs derived from rRNA—typically present in high abundance following cDNA synthesis from total RNA inputs—makes the workflow extremely sensitive, yielding data that is highly reproducible with low mapping to rRNA. The new library design featured in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian improves sequencing performance compared to the original SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian, particularly for NextSeq® and MiniSeq™ instruments carrying the two-channel SBS technology. This kit includes the Indexing Primer Set HT for Illumina v2; for your convenience, we also offer the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Components (Cat. #s 634418 and 634419) without indexing primers.

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.

Documents Components Image Data

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Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Structural features of final libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. The adapters added using 5' PCR Primer HT and 3' PCR Primer HT contain sequences allowing clustering on any Illumina® flow cell (P7 shown in light blue, P5 shown in red), Illumina TruSeq® HT indexes (Index 1 [i7] sequence shown in orange, and Index 2 [i5] sequence shown in yellow), as well as the regions recognized by sequencing primers Read Primer 2 (Read 2, purple) and Read Primer 1 (Read 1, green). Read 1 generates sequences antisense to the original RNA, while Read 2 yields sequences sense to the original RNA (orientation of original RNA denoted by 5' and 3' in dark blue). The first three nucleotides of the second sequencing read (Read 2) are derived from the Pico v2 SMART Adapter (shown as Xs). These three nucleotides must be trimmed prior to mapping if performing paired-end sequencing.

Back

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved pass-filter rates (%PF) with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Libraries generated with the Pico v1 or Pico v2 kits were pooled and run on NextSeq 500 or MiniSeq instruments, as indicated. For each graph, blue boxplots indicate the distribution of cluster densities for unfiltered (i.e., raw) reads, while the green boxplots indicate the distribution of cluster densities for reads that passed filtering. Quantities of reads passing filter (in millions) and %PF values for each sequencing run are included above each graph. The expected number of reads passing filter according to Illumina specifications was 130 million reads for runs on the NextSeq and 25 million reads for runs on the MiniSeq. Proportions of reads that aligned to PhiX sequences ranged from 0.5% to 1.15% for all sequencing runs. As indicated in the graphs, libraries generated with the Pico v2 kit achieved higher %PF values for both Illumina platforms relative to libraries generated with the Pico v1 kit, and yielded quantities of reads passing filter that greatly exceeded the Illumina specifications.

Back

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of technology in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. SMART technology is used in this ligation-free protocol to preserve strand-of-origin information. Random priming (represented as the green N6 Primer) allows the generation of cDNA from all RNA fragments in the sample, including rRNA. When the SMARTScribe Reverse Transcriptase (RT) reaches the 5' end of the RNA fragment, the enzyme’s terminal transferase activity adds a few non-templated nucleotides to the 3' end of the cDNA (shown as Xs). The carefully designed Pico v2 SMART Adapter (included in the SMART TSO Mix v2) base-pairs with the non-templated nucleotide stretch, creating an extended template to enable the RT to continue replicating to the end of the oligonucleotide. The resulting cDNA contains sequences derived from the random primer and the Pico v2 SMART Adapter used in the reverse transcription reaction. In the next step, a first round of PCR amplification (PCR1) adds full-length Illumina adapters, including barcodes. The 5' PCR Primer binds to the Pico v2 SMART Adapter sequence (light purple), while the 3' PCR Primer binds to sequence associated with the random primer (green). The ribosomal cDNA (originating from rRNA) is then cleaved by ZapR v2 in the presence of the mammalian-specific R-Probes v2. This process leaves the library fragments originating from non-rRNA molecules untouched, with priming sites available on both 5' and 3' ends for further PCR amplification. These fragments are enriched via a second round of PCR amplification (PCR2) using primers universal to all libraries. The final library contains sequences allowing clustering on any Illumina flow cell.

Back

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sensitivity and reproducibility with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Sequencing libraries were generated from 1 ng and 10 ng inputs of total RNA extracted from human lung FFPE tissue using both the Pico v1 and Pico v2 kits, and sequenced on a NextSeq 500 instrument. Panel A. Sequencing metrics for libraries generated from 1 ng or 10 ng inputs using each kit. For both input amounts, the Pico v2 kit resulted in greater library yields, a lower proportion of reads mapping to rRNA and mtRNA, and a lower duplicate rate. For the 1 ng input, sequencing data from the Pico v2 library also identified thousands more transcripts than sequencing data from the Pico v1 library, indicating a higher sensitivity for Pico v2. Panel B. Comparison of transcript expression levels across input amounts. Higher reproducibility was observed between 1 ng and 10 ng inputs for data generated with the Pico v2 kit vs. data generated using the Pico v1 kit. FPKM values are shown on a Log10 scale. Transcripts represented in only one library can be seen along the X- and Y-axes of the scatter plots.

Back

SeqAmp CB PCR buffer improves bead-pellet formation

SeqAmp CB PCR buffer improves bead-pellet formation

Improved bead-pellet formation with new SeqAmp CB PCR buffer. The PCR buffer included in the Pico v2 kit was re-formulated to allow for faster, tighter bead-pellet formation. Following magnetic separation for a fixed period, bead pellets formed in the new SeqAmp CB buffer (right) are tighter than those formed in the original PCR buffer (left). Tighter bead pellets tend to dry more evenly and are easier to resuspend than pellets that are broader and more diffuse.

Back

SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Product Photo: 12 Rxns (634411)

SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Product Photo: 12 Rxns (634411)
634412 SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian 48 Rxns USD $3516.00

License Statement

ID Number  
391 LIMITED USE LABEL LICENSE: RESEARCH USE ONLY Notice to Purchaser: This product is subject to a license granted to Takara Bio USA, Inc. and its Affiliates from Caribou Biosciences, Inc., and this product is transferred to the end-user purchaser (“Purchaser”) subject to a “Limited Use Label License” conveying to the Purchaser a limited, non-transferable right to use the product, solely as provided to Purchaser, together with (i) progeny or derivatives of the product generated by the Purchaser (including but not limited to cells), and (ii) biological material extracted or derived from the product or its corresponding progeny or derivatives (including but not limited to cells) (collectively, the product, and (i) and (ii) are referred to as “Material”) only to perform internal research for the sole benefit of the Purchaser. The Purchaser cannot sell or otherwise transfer Material to a third party or otherwise use the Material for any Excluded Use. “Excluded Use” means any and all: (a) commercial activity including, but not limited to, any use in manufacturing (including but not limited to cell line development for purposes of bioproduction), product testing, or quality control; (b) preclinical or clinical testing or other activity directed toward the submission of data to the U.S. Food and Drug Administration, or any other regulatory agency in any country or jurisdiction where the active agent in such studies comprises the Material; (c) use to provide a service, information, or data to a third party; (d) use for human or animal therapeutic, diagnostic, or prophylactic purposes or as a product for therapeutics, diagnostics, or prophylaxis; (e) activity in an agricultural field trial or any activity directed toward the submission of data to the U.S. Department of Agriculture or any other agriculture regulatory agency; (f) high throughput screening drug discovery purposes (i.e., the screening of more than 10,000 experiments per day) as well as scale-up production activities for commercialization; (g) modification of human germline, including editing of human embryo genomes (with the sole exception of editing human embryonic stem (ES) cell lines for research purposes) or reproductive cells; (h) self-editing; and/or (i) stimulation of biased inheritance of a particular gene or trait or set of genes or traits (“gene drive”). It is the Purchaser’s responsibility to use the Material in accordance with all applicable laws and regulations. For information on obtaining additional rights, including commercial rights, please contact licensing@cariboubio.com or Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA 94710 USA, Attn: Licensing.
395 This product is protected by U.S. Patent No. 10150985 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 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian is used to generate strand-specific RNA-seq libraries for Illumina sequencing from 250 pg–10 ng inputs of purified total RNA. This kit incorporates Takara Bio’s proprietary SMART (Switching Mechanism at the 5’ end of RNA Template) technology and includes refinements to the SMARTer method for stranded RNA-seq that simplify the library preparation workflow and improve sequencing performance. This method was developed to work with either high- or low-quality total RNA, does not require additional rRNA removal methods or kits, and produces sequencing libraries that retain strand-of-origin information. The integrated removal of cDNAs derived from rRNA—typically present in high abundance following cDNA synthesis from total RNA inputs—makes the workflow extremely sensitive, yielding data that is highly reproducible with low mapping to rRNA. The new library design featured in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian improves sequencing performance compared to the original SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian, particularly for NextSeq® and MiniSeq™ instruments carrying the two-channel SBS technology. This kit includes the Indexing Primer Set HT for Illumina v2; for your convenience, we also offer the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Components (Cat. #s 634418 and 634419) without indexing primers.

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.

Documents Components Image Data

Back

Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Structural features of final libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. The adapters added using 5' PCR Primer HT and 3' PCR Primer HT contain sequences allowing clustering on any Illumina® flow cell (P7 shown in light blue, P5 shown in red), Illumina TruSeq® HT indexes (Index 1 [i7] sequence shown in orange, and Index 2 [i5] sequence shown in yellow), as well as the regions recognized by sequencing primers Read Primer 2 (Read 2, purple) and Read Primer 1 (Read 1, green). Read 1 generates sequences antisense to the original RNA, while Read 2 yields sequences sense to the original RNA (orientation of original RNA denoted by 5' and 3' in dark blue). The first three nucleotides of the second sequencing read (Read 2) are derived from the Pico v2 SMART Adapter (shown as Xs). These three nucleotides must be trimmed prior to mapping if performing paired-end sequencing.

Back

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved pass-filter rates (%PF) with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Libraries generated with the Pico v1 or Pico v2 kits were pooled and run on NextSeq 500 or MiniSeq instruments, as indicated. For each graph, blue boxplots indicate the distribution of cluster densities for unfiltered (i.e., raw) reads, while the green boxplots indicate the distribution of cluster densities for reads that passed filtering. Quantities of reads passing filter (in millions) and %PF values for each sequencing run are included above each graph. The expected number of reads passing filter according to Illumina specifications was 130 million reads for runs on the NextSeq and 25 million reads for runs on the MiniSeq. Proportions of reads that aligned to PhiX sequences ranged from 0.5% to 1.15% for all sequencing runs. As indicated in the graphs, libraries generated with the Pico v2 kit achieved higher %PF values for both Illumina platforms relative to libraries generated with the Pico v1 kit, and yielded quantities of reads passing filter that greatly exceeded the Illumina specifications.

Back

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of technology in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. SMART technology is used in this ligation-free protocol to preserve strand-of-origin information. Random priming (represented as the green N6 Primer) allows the generation of cDNA from all RNA fragments in the sample, including rRNA. When the SMARTScribe Reverse Transcriptase (RT) reaches the 5' end of the RNA fragment, the enzyme’s terminal transferase activity adds a few non-templated nucleotides to the 3' end of the cDNA (shown as Xs). The carefully designed Pico v2 SMART Adapter (included in the SMART TSO Mix v2) base-pairs with the non-templated nucleotide stretch, creating an extended template to enable the RT to continue replicating to the end of the oligonucleotide. The resulting cDNA contains sequences derived from the random primer and the Pico v2 SMART Adapter used in the reverse transcription reaction. In the next step, a first round of PCR amplification (PCR1) adds full-length Illumina adapters, including barcodes. The 5' PCR Primer binds to the Pico v2 SMART Adapter sequence (light purple), while the 3' PCR Primer binds to sequence associated with the random primer (green). The ribosomal cDNA (originating from rRNA) is then cleaved by ZapR v2 in the presence of the mammalian-specific R-Probes v2. This process leaves the library fragments originating from non-rRNA molecules untouched, with priming sites available on both 5' and 3' ends for further PCR amplification. These fragments are enriched via a second round of PCR amplification (PCR2) using primers universal to all libraries. The final library contains sequences allowing clustering on any Illumina flow cell.

Back

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sensitivity and reproducibility with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Sequencing libraries were generated from 1 ng and 10 ng inputs of total RNA extracted from human lung FFPE tissue using both the Pico v1 and Pico v2 kits, and sequenced on a NextSeq 500 instrument. Panel A. Sequencing metrics for libraries generated from 1 ng or 10 ng inputs using each kit. For both input amounts, the Pico v2 kit resulted in greater library yields, a lower proportion of reads mapping to rRNA and mtRNA, and a lower duplicate rate. For the 1 ng input, sequencing data from the Pico v2 library also identified thousands more transcripts than sequencing data from the Pico v1 library, indicating a higher sensitivity for Pico v2. Panel B. Comparison of transcript expression levels across input amounts. Higher reproducibility was observed between 1 ng and 10 ng inputs for data generated with the Pico v2 kit vs. data generated using the Pico v1 kit. FPKM values are shown on a Log10 scale. Transcripts represented in only one library can be seen along the X- and Y-axes of the scatter plots.

Back

SeqAmp CB PCR buffer improves bead-pellet formation

SeqAmp CB PCR buffer improves bead-pellet formation

Improved bead-pellet formation with new SeqAmp CB PCR buffer. The PCR buffer included in the Pico v2 kit was re-formulated to allow for faster, tighter bead-pellet formation. Following magnetic separation for a fixed period, bead pellets formed in the new SeqAmp CB buffer (right) are tighter than those formed in the original PCR buffer (left). Tighter bead pellets tend to dry more evenly and are easier to resuspend than pellets that are broader and more diffuse.

634413 SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian 96 Rxns USD $4623.00

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391 LIMITED USE LABEL LICENSE: RESEARCH USE ONLY Notice to Purchaser: This product is subject to a license granted to Takara Bio USA, Inc. and its Affiliates from Caribou Biosciences, Inc., and this product is transferred to the end-user purchaser (“Purchaser”) subject to a “Limited Use Label License” conveying to the Purchaser a limited, non-transferable right to use the product, solely as provided to Purchaser, together with (i) progeny or derivatives of the product generated by the Purchaser (including but not limited to cells), and (ii) biological material extracted or derived from the product or its corresponding progeny or derivatives (including but not limited to cells) (collectively, the product, and (i) and (ii) are referred to as “Material”) only to perform internal research for the sole benefit of the Purchaser. The Purchaser cannot sell or otherwise transfer Material to a third party or otherwise use the Material for any Excluded Use. “Excluded Use” means any and all: (a) commercial activity including, but not limited to, any use in manufacturing (including but not limited to cell line development for purposes of bioproduction), product testing, or quality control; (b) preclinical or clinical testing or other activity directed toward the submission of data to the U.S. Food and Drug Administration, or any other regulatory agency in any country or jurisdiction where the active agent in such studies comprises the Material; (c) use to provide a service, information, or data to a third party; (d) use for human or animal therapeutic, diagnostic, or prophylactic purposes or as a product for therapeutics, diagnostics, or prophylaxis; (e) activity in an agricultural field trial or any activity directed toward the submission of data to the U.S. Department of Agriculture or any other agriculture regulatory agency; (f) high throughput screening drug discovery purposes (i.e., the screening of more than 10,000 experiments per day) as well as scale-up production activities for commercialization; (g) modification of human germline, including editing of human embryo genomes (with the sole exception of editing human embryonic stem (ES) cell lines for research purposes) or reproductive cells; (h) self-editing; and/or (i) stimulation of biased inheritance of a particular gene or trait or set of genes or traits (“gene drive”). It is the Purchaser’s responsibility to use the Material in accordance with all applicable laws and regulations. For information on obtaining additional rights, including commercial rights, please contact licensing@cariboubio.com or Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA 94710 USA, Attn: Licensing.
395 This product is protected by U.S. Patent No. 10150985 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 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian is used to generate strand-specific RNA-seq libraries for Illumina sequencing from 250 pg–10 ng inputs of purified total RNA. This kit incorporates Takara Bio’s proprietary SMART (Switching Mechanism at the 5’ end of RNA Template) technology and includes refinements to the SMARTer method for stranded RNA-seq that simplify the library preparation workflow and improve sequencing performance. This method was developed to work with either high- or low-quality total RNA, does not require additional rRNA removal methods or kits, and produces sequencing libraries that retain strand-of-origin information. The integrated removal of cDNAs derived from rRNA—typically present in high abundance following cDNA synthesis from total RNA inputs—makes the workflow extremely sensitive, yielding data that is highly reproducible with low mapping to rRNA. The new library design featured in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian improves sequencing performance compared to the original SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian, particularly for NextSeq® and MiniSeq™ instruments carrying the two-channel SBS technology. This kit includes the Indexing Primer Set HT for Illumina v2; for your convenience, we also offer the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Components (Cat. #s 634418 and 634419) without indexing primers.

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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Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Structural features of final libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. The adapters added using 5' PCR Primer HT and 3' PCR Primer HT contain sequences allowing clustering on any Illumina® flow cell (P7 shown in light blue, P5 shown in red), Illumina TruSeq® HT indexes (Index 1 [i7] sequence shown in orange, and Index 2 [i5] sequence shown in yellow), as well as the regions recognized by sequencing primers Read Primer 2 (Read 2, purple) and Read Primer 1 (Read 1, green). Read 1 generates sequences antisense to the original RNA, while Read 2 yields sequences sense to the original RNA (orientation of original RNA denoted by 5' and 3' in dark blue). The first three nucleotides of the second sequencing read (Read 2) are derived from the Pico v2 SMART Adapter (shown as Xs). These three nucleotides must be trimmed prior to mapping if performing paired-end sequencing.

Back

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved pass-filter rates (%PF) with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Libraries generated with the Pico v1 or Pico v2 kits were pooled and run on NextSeq 500 or MiniSeq instruments, as indicated. For each graph, blue boxplots indicate the distribution of cluster densities for unfiltered (i.e., raw) reads, while the green boxplots indicate the distribution of cluster densities for reads that passed filtering. Quantities of reads passing filter (in millions) and %PF values for each sequencing run are included above each graph. The expected number of reads passing filter according to Illumina specifications was 130 million reads for runs on the NextSeq and 25 million reads for runs on the MiniSeq. Proportions of reads that aligned to PhiX sequences ranged from 0.5% to 1.15% for all sequencing runs. As indicated in the graphs, libraries generated with the Pico v2 kit achieved higher %PF values for both Illumina platforms relative to libraries generated with the Pico v1 kit, and yielded quantities of reads passing filter that greatly exceeded the Illumina specifications.

Back

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of technology in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. SMART technology is used in this ligation-free protocol to preserve strand-of-origin information. Random priming (represented as the green N6 Primer) allows the generation of cDNA from all RNA fragments in the sample, including rRNA. When the SMARTScribe Reverse Transcriptase (RT) reaches the 5' end of the RNA fragment, the enzyme’s terminal transferase activity adds a few non-templated nucleotides to the 3' end of the cDNA (shown as Xs). The carefully designed Pico v2 SMART Adapter (included in the SMART TSO Mix v2) base-pairs with the non-templated nucleotide stretch, creating an extended template to enable the RT to continue replicating to the end of the oligonucleotide. The resulting cDNA contains sequences derived from the random primer and the Pico v2 SMART Adapter used in the reverse transcription reaction. In the next step, a first round of PCR amplification (PCR1) adds full-length Illumina adapters, including barcodes. The 5' PCR Primer binds to the Pico v2 SMART Adapter sequence (light purple), while the 3' PCR Primer binds to sequence associated with the random primer (green). The ribosomal cDNA (originating from rRNA) is then cleaved by ZapR v2 in the presence of the mammalian-specific R-Probes v2. This process leaves the library fragments originating from non-rRNA molecules untouched, with priming sites available on both 5' and 3' ends for further PCR amplification. These fragments are enriched via a second round of PCR amplification (PCR2) using primers universal to all libraries. The final library contains sequences allowing clustering on any Illumina flow cell.

Back

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sensitivity and reproducibility with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Sequencing libraries were generated from 1 ng and 10 ng inputs of total RNA extracted from human lung FFPE tissue using both the Pico v1 and Pico v2 kits, and sequenced on a NextSeq 500 instrument. Panel A. Sequencing metrics for libraries generated from 1 ng or 10 ng inputs using each kit. For both input amounts, the Pico v2 kit resulted in greater library yields, a lower proportion of reads mapping to rRNA and mtRNA, and a lower duplicate rate. For the 1 ng input, sequencing data from the Pico v2 library also identified thousands more transcripts than sequencing data from the Pico v1 library, indicating a higher sensitivity for Pico v2. Panel B. Comparison of transcript expression levels across input amounts. Higher reproducibility was observed between 1 ng and 10 ng inputs for data generated with the Pico v2 kit vs. data generated using the Pico v1 kit. FPKM values are shown on a Log10 scale. Transcripts represented in only one library can be seen along the X- and Y-axes of the scatter plots.

Back

SeqAmp CB PCR buffer improves bead-pellet formation

SeqAmp CB PCR buffer improves bead-pellet formation

Improved bead-pellet formation with new SeqAmp CB PCR buffer. The PCR buffer included in the Pico v2 kit was re-formulated to allow for faster, tighter bead-pellet formation. Following magnetic separation for a fixed period, bead pellets formed in the new SeqAmp CB buffer (right) are tighter than those formed in the original PCR buffer (left). Tighter bead pellets tend to dry more evenly and are easier to resuspend than pellets that are broader and more diffuse.

Back

SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Product Photo: 96 Rxns (634413)

SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Product Photo: 96 Rxns (634413)
634414 SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian 192 Rxns USD $8321.00

License Statement

ID Number  
391 LIMITED USE LABEL LICENSE: RESEARCH USE ONLY Notice to Purchaser: This product is subject to a license granted to Takara Bio USA, Inc. and its Affiliates from Caribou Biosciences, Inc., and this product is transferred to the end-user purchaser (“Purchaser”) subject to a “Limited Use Label License” conveying to the Purchaser a limited, non-transferable right to use the product, solely as provided to Purchaser, together with (i) progeny or derivatives of the product generated by the Purchaser (including but not limited to cells), and (ii) biological material extracted or derived from the product or its corresponding progeny or derivatives (including but not limited to cells) (collectively, the product, and (i) and (ii) are referred to as “Material”) only to perform internal research for the sole benefit of the Purchaser. The Purchaser cannot sell or otherwise transfer Material to a third party or otherwise use the Material for any Excluded Use. “Excluded Use” means any and all: (a) commercial activity including, but not limited to, any use in manufacturing (including but not limited to cell line development for purposes of bioproduction), product testing, or quality control; (b) preclinical or clinical testing or other activity directed toward the submission of data to the U.S. Food and Drug Administration, or any other regulatory agency in any country or jurisdiction where the active agent in such studies comprises the Material; (c) use to provide a service, information, or data to a third party; (d) use for human or animal therapeutic, diagnostic, or prophylactic purposes or as a product for therapeutics, diagnostics, or prophylaxis; (e) activity in an agricultural field trial or any activity directed toward the submission of data to the U.S. Department of Agriculture or any other agriculture regulatory agency; (f) high throughput screening drug discovery purposes (i.e., the screening of more than 10,000 experiments per day) as well as scale-up production activities for commercialization; (g) modification of human germline, including editing of human embryo genomes (with the sole exception of editing human embryonic stem (ES) cell lines for research purposes) or reproductive cells; (h) self-editing; and/or (i) stimulation of biased inheritance of a particular gene or trait or set of genes or traits (“gene drive”). It is the Purchaser’s responsibility to use the Material in accordance with all applicable laws and regulations. For information on obtaining additional rights, including commercial rights, please contact licensing@cariboubio.com or Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA 94710 USA, Attn: Licensing.
395 This product is protected by U.S. Patent No. 10150985 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 SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian is used to generate strand-specific RNA-seq libraries for Illumina sequencing from 250 pg–10 ng inputs of purified total RNA. This kit incorporates Takara Bio’s proprietary SMART (Switching Mechanism at the 5’ end of RNA Template) technology and includes refinements to the SMARTer method for stranded RNA-seq that simplify the library preparation workflow and improve sequencing performance. This method was developed to work with either high- or low-quality total RNA, does not require additional rRNA removal methods or kits, and produces sequencing libraries that retain strand-of-origin information. The integrated removal of cDNAs derived from rRNA—typically present in high abundance following cDNA synthesis from total RNA inputs—makes the workflow extremely sensitive, yielding data that is highly reproducible with low mapping to rRNA. The new library design featured in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian improves sequencing performance compared to the original SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian, particularly for NextSeq® and MiniSeq™ instruments carrying the two-channel SBS technology. This kit includes the Indexing Primer Set HT for Illumina v2; for your convenience, we also offer the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian Components (Cat. #s 634418 and 634419) without indexing primers.

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.

Documents Components Image Data

Back

Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of sequencing libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Structural features of final libraries generated with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. The adapters added using 5' PCR Primer HT and 3' PCR Primer HT contain sequences allowing clustering on any Illumina® flow cell (P7 shown in light blue, P5 shown in red), Illumina TruSeq® HT indexes (Index 1 [i7] sequence shown in orange, and Index 2 [i5] sequence shown in yellow), as well as the regions recognized by sequencing primers Read Primer 2 (Read 2, purple) and Read Primer 1 (Read 1, green). Read 1 generates sequences antisense to the original RNA, while Read 2 yields sequences sense to the original RNA (orientation of original RNA denoted by 5' and 3' in dark blue). The first three nucleotides of the second sequencing read (Read 2) are derived from the Pico v2 SMART Adapter (shown as Xs). These three nucleotides must be trimmed prior to mapping if performing paired-end sequencing.

Back

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing performance with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved pass-filter rates (%PF) with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Libraries generated with the Pico v1 or Pico v2 kits were pooled and run on NextSeq 500 or MiniSeq instruments, as indicated. For each graph, blue boxplots indicate the distribution of cluster densities for unfiltered (i.e., raw) reads, while the green boxplots indicate the distribution of cluster densities for reads that passed filtering. Quantities of reads passing filter (in millions) and %PF values for each sequencing run are included above each graph. The expected number of reads passing filter according to Illumina specifications was 130 million reads for runs on the NextSeq and 25 million reads for runs on the MiniSeq. Proportions of reads that aligned to PhiX sequences ranged from 0.5% to 1.15% for all sequencing runs. As indicated in the graphs, libraries generated with the Pico v2 kit achieved higher %PF values for both Illumina platforms relative to libraries generated with the Pico v1 kit, and yielded quantities of reads passing filter that greatly exceeded the Illumina specifications.

Back

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Workflow for SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Schematic of technology in the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. SMART technology is used in this ligation-free protocol to preserve strand-of-origin information. Random priming (represented as the green N6 Primer) allows the generation of cDNA from all RNA fragments in the sample, including rRNA. When the SMARTScribe Reverse Transcriptase (RT) reaches the 5' end of the RNA fragment, the enzyme’s terminal transferase activity adds a few non-templated nucleotides to the 3' end of the cDNA (shown as Xs). The carefully designed Pico v2 SMART Adapter (included in the SMART TSO Mix v2) base-pairs with the non-templated nucleotide stretch, creating an extended template to enable the RT to continue replicating to the end of the oligonucleotide. The resulting cDNA contains sequences derived from the random primer and the Pico v2 SMART Adapter used in the reverse transcription reaction. In the next step, a first round of PCR amplification (PCR1) adds full-length Illumina adapters, including barcodes. The 5' PCR Primer binds to the Pico v2 SMART Adapter sequence (light purple), while the 3' PCR Primer binds to sequence associated with the random primer (green). The ribosomal cDNA (originating from rRNA) is then cleaved by ZapR v2 in the presence of the mammalian-specific R-Probes v2. This process leaves the library fragments originating from non-rRNA molecules untouched, with priming sites available on both 5' and 3' ends for further PCR amplification. These fragments are enriched via a second round of PCR amplification (PCR2) using primers universal to all libraries. The final library contains sequences allowing clustering on any Illumina flow cell.

Back

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sequencing metrics with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

Improved sensitivity and reproducibility with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. Sequencing libraries were generated from 1 ng and 10 ng inputs of total RNA extracted from human lung FFPE tissue using both the Pico v1 and Pico v2 kits, and sequenced on a NextSeq 500 instrument. Panel A. Sequencing metrics for libraries generated from 1 ng or 10 ng inputs using each kit. For both input amounts, the Pico v2 kit resulted in greater library yields, a lower proportion of reads mapping to rRNA and mtRNA, and a lower duplicate rate. For the 1 ng input, sequencing data from the Pico v2 library also identified thousands more transcripts than sequencing data from the Pico v1 library, indicating a higher sensitivity for Pico v2. Panel B. Comparison of transcript expression levels across input amounts. Higher reproducibility was observed between 1 ng and 10 ng inputs for data generated with the Pico v2 kit vs. data generated using the Pico v1 kit. FPKM values are shown on a Log10 scale. Transcripts represented in only one library can be seen along the X- and Y-axes of the scatter plots.

Back

SeqAmp CB PCR buffer improves bead-pellet formation

SeqAmp CB PCR buffer improves bead-pellet formation

Improved bead-pellet formation with new SeqAmp CB PCR buffer. The PCR buffer included in the Pico v2 kit was re-formulated to allow for faster, tighter bead-pellet formation. Following magnetic separation for a fixed period, bead pellets formed in the new SeqAmp CB buffer (right) are tighter than those formed in the original PCR buffer (left). Tighter bead pellets tend to dry more evenly and are easier to resuspend than pellets that are broader and more diffuse.

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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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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.

FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES (EXCEPT AS SPECIFICALLY NOTED).

Clontech, TaKaRa, cellartis

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