Differential expression analysis on the ICELL8 Single-Cell System
By leveraging Takara Bio's expertise in single-cell RNA-seq library construction and the cell isolation and selection capabilities of the ICELL8 platform, the ICELL8 3' DE and ICELL8 3' DE for UMI workflows enable high-throughput preparation of Illumina libraries for differential expression analysis of single cells from up to eight different samples in parallel.
By leveraging Takara Bio's expertise in single-cell RNA-seq library construction and the cell isolation and selection capabilities of ICELL8 systems, the ICELL8 3' DE and ICELL8 3' DE for UMI workflows enable high-throughput preparation of Illumina libraries for differential expression analysis of single cells from up to eight different samples in parallel.
The ICELL8 Chip and Reagent 3' DE Kit (Cat. # 640164, 640165, 640166) is compatible with the original ICELL8 Single-Cell System. Included in the kit are an ICELL8 3' DE Chip (Cat. # 640143), a 5,184-nanowell SmartChip that contains preprinted oligo(dT) primers, and reagents for cDNA synthesis and Illumina library prep.
Following staining and dilution, sample cells are dispensed into chip nanowells using the ICELL8 MultiSample NanoDispenser (MSND). Wells containing single, viable cells are selected using the ICELL8 Imaging System and the CellSelect Software provided with the ICELL8 system. Following the selection of cells for processing and analysis, RT-PCR reagents are dispensed into the corresponding wells, and cDNA synthesis and amplification are performed in-chip in a single run. Following RT-PCR, cDNA products are pooled and purified, and sequencing libraries are prepared using a transposase-based method that enriches for cDNA derived from mRNA 3' ends, followed by a limited-cycle PCR amplification step that incorporates Illumina index sequences.
Sequencing data from the resulting libraries can be traced back to individual cells using the nanowell-specific barcode sequences and can be used to perform differential gene expression analysis by mRNA 3' end-counting. By yielding high-quality, 3'-focused sequencing data from hundreds of cells in parallel, these kits provide an efficient, cost-effective solution for high-throughput differential expression analysis of single cells.
The ICELL8 3' DE for UMI Reagent Kit is used with the ICELL8 3' DE Chip as part of the ICELL8 3' DE with UMI workflow, which enables Illumina sequencing and differential gene expression analysis-via transcript 3' end counting-of single cells isolated on the ICELL8 system.
Overview
- High-throughput single-cell analysis—generate sequencing data from hundreds of single cells in parallel
- Sample flexibility—analyze cells from up to eight different samples in a single experiment
- mRNA 3' sequence enrichment—reduce the number of reads required for differential gene expression analysis by enriching for sequences derived from mRNA 3' ends
- Reduced sample handling—minimize variability with automated cell isolation and selection, and sample pooling prior to library construction
- Illumina sequencing libraries—generate libraries suitable for sequencing on all Illumina platforms
NOTE: The procedures for each 3' DE kit vary, so be sure to reference the appropriate user manual.
More Information
Components
The following items are required to complete the workflow:
| ICELL8 3′ DE workflow | ||
|---|---|---|
| Cat. # | Product | 1 item required per: |
| 640167 | ICELL8 3' DE Reagent Kit | 1 chip |
| 640143 | ICELL8 3' DE Chip | 1 run |
| 640048 | ICELL8 Collection Kit | 1 chip |
| 640109 | ICELL8 Loading Kit | 1 chip |
| 640018 | MSND 384-Well Source Plate and Seals* (20/pack) | 10 chips |
| 640037 | MSND 384-Well Source Plate and Seals* (120/pack) | 60 chips |
| Other available kit packages that include chip(s), reagent kit, loading kit, and collection kit | ||
| 640164 | ICELL8 Chip and Reagent 3' DE Kit | 1 chip (contained in kit) |
| 640165 | ICELL8 Chip and Reagent 3' DE Kit | 3 chips (contained in kit) |
| 640166 | ICELL8 Chip and Reagent 3' DE Kit | 5 chips (contained in kit) |
| ICELL8 3′ DE for UMI workflow | ||
|---|---|---|
| Cat. # | Product | 1 item required per: |
| 640005 | ICELL8 3' DE for UMI Reagent Kit | 1 chip |
| 640143 | ICELL8 3' DE Chip | 1 run |
| 640048 | ICELL8 Collection Kit | 1 chip |
| 640109 | ICELL8 Loading Kit | 1 chip |
| 640018 | MSND 384-Well Source Plate and Seals* (20/pack) | 10 chips |
| 640037 | MSND 384-Well Source Plate and Seals* (120/pack) | 60 chips |
*Note: Cat. No. 640018 contains enough plates and film for 10 chips. If you plan on processing more chips, Cat. No. 640037 has enough plates and sealing film for up to 60 chips.
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.
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Comparing single-cell RNA-seq on automation platforms
Which systems should you trust with your single-cell RNA-seq experiments? This blog post discusses a comprehensive study performed by the Association of Biomolecular Resource Facilities (ABRF) Genomics Research Group (GRG), in which the performance of automated, single-cell NGS platforms from several providers were compared in head-to-head experiments. The ICELL8 Single Cell System with 3' (DE) expression profiling excelled in important data-quality metrics, including sensitivity, read efficiency, and gene diversity.
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