Takara Bio's platform (teal) performed significantly better than 10X Genomics' platform.

Two conditions were tested on the 10X Genomics Chromium system: 10X fresh (pink), with immediate processing, and 10X shipped (purple), with processing after overnight shipment. Excellent success rate (gene detection) for scRNA-seq with the Takara Bio ICELL8 Single-Cell System. Overall, the median number of genes detected by the ICELL8 system surpassed that of 10X Genomics, under both conditions, and that of the Illumina Bio-Rad ddSEQ.įigure 1. Approximately twice as many genes were detected with the ICELL8 system as the 10X Genomics system. When it comes to sensitivity, or the ability to detect distinct genes, the ICELL8 system performs significantly better than the best data from 10X Chromium (Figure 1, below). Moreover, the ICELL8 system excelled in important data-quality metrics: sensitivity, read efficiency, and gene diversity.

(Update: we have since developed a full-length scRNA-seq workflow!) The ICELL8 system had a total cell-capture and library-generation time that was significantly lower than other platforms: 7 hr on ICELL8 system versus 12 hr on Fluidigm C1 HT and 10 hr each on Fluidigm 96 IFC, 10X Chromium, and Illumina/Bio-Rad ddSEQ. The ABRF GRG noted that this system monitors cells (with a capture capacity of up to 1,800 cells), does not have cell-size dependence, has a good cell capture efficiency, and uses 3' expression (DE) profiling. The ICELL8 system stood out as the only system using an ordered array. The findingsĪs the only system to utilize a nanodispensing array, the Takara Bio ICELL8 system enables high-throughput processing of hundreds of single cells in a heterogeneous population without the common microfluidic cell-size constraints or the imaging limitations of droplet-based systems, thereby reducing sample-handling artifacts. Bulk RNA-seq was performed on a subset of cells from each treatment condition. Single cells were captured and libraries prepared using each platform's technology. The ABRF GRG generated data from hundreds of individual SUM149PT cells (breast cancer cell line) treated with the histone deacetylase inhibitor TSA or vehicle control (DMSO). The authors set out to compare technologies and data quality between notable single-cell NGS library prep systems: Fluidigm C1 (96 IFC and HT-IFC), 10X Genomics Chromium Controller, Illumina Bio-Rad ddSEQ, and Takara Bio ICELL8 Single-Cell System.

They presented their in-depth results at the ABRF 2018 conference in a poster titled 'Comparative analysis of single-cell RNA sequencing platforms and methods.' Comparison of scRNA-seq platforms The Association of Biomolecular Resource Facilities (ABRF) Genomics Research Group (GRG) performed a comprehensive study to evaluate platforms from Fluidigm, 10X Genomics, Illumina Bio-Rad, and Takara Bio. What are the differences between these platforms, and how do they impact your data?Ī head-to-head performance comparison can help determine which systems to trust for your single-cell RNA-seq (scRNA-seq) experiments. Several platforms have emerged to meet this need but variations in the underlying technology-such as microfluidics, droplet encapsulation, or multisample nanodispensing-influence how the single cells are captured and processed. The use of next-generation sequencing for transcriptome analysis in clinical and applied spaces requires accurate, parallel processing of large numbers of single cells.

10x chromium system