ddSEQ™ Single-Cell Isolator

ddSEQ™ Single-Cell Isolator


Single-Cell Sequencing
Unbiased, Cell-Size Agnostic RNA-Seq

Mouse cell lines (A20, NIH3T3) and human cell lines (HEK, BJ) were processed using the SureCell WTA 3'Library Prep Kit. Consistently high numbers of detected genes demonstrate that recovery of transcripts is not limited by cell size.


Confident Single-Cell Transcript Identification

A. BaseSpace generated plots of the number of unique molecular identifiers (UMI), i.e. transcripts, assigned to the mouse/mm10 (red) and human/hg19 (blue) genomes for each cell barcode. Unique transcripts mapping to both mouse and human (purple) represent cell doublets. B. Cumulated fraction of unique transcripts assigned to cell barcodes (linear scale). The inflection point (red line) determines the number of barcoded cells detected in the sequencing run.


Confident Cell Subpopulation Identification

A. Analysis in the Single-Cell RNA-Seq BaseSpace App using the t-SNE algorithm of a mixture of NIH 3T3 and HEK 293 cells identifies a distinct subpopulation of cells. B. Cells color coded by gene expression of hg19 RPL 13 confirms the identity of the subpopulation as human.


Cell Cycle Analysis of Single Cells by RNA-Seq

Analysis of cell cycle state using the Single-Cell RNA-Seq BaseSpace App is based on unique transcript counts of genes associated with each phase of the cell cycle, normalized by the total count for each cell. Expression is centered by the median and scaled by the median absolute deviation for each cell cycle.


Speak with a Specialist about your sequencing needs

ddSEQ Speak with a Specialist

The ddSEQ Single-Cell Isolator is part of the Illumina® Bio-Rad® Single-Cell Sequencing Solution, a platform that brings Bio-Rad's Droplet Digital™ technology and Illumina's market-leading sequencing expertise to single-cell gene expression studies.

The ddSEQ Single-Cell Isolator works with the Illumina® Bio-Rad® SureCell™ WTA 3' Library Prep Kit for the ddSEQ™ System. This technology utilizes disposable microfluidic cartridges to coencapsulate single cells and barcodes into subnanoliter droplets, where cell lysis and barcoding occur. RNA-Seq libraries are subsequently prepared and sequenced. Analysis is conducted via BaseSpace.

Features and Benefits

  • Process hundreds to tens of thousands of cells per day
  • Sensitive and unbiased characterization of transcriptional signatures
  • Scalable solution to accommodate a wide range of experimental designs
  • Agnostic to mammalian cell size, enabling unbiased profiling of diverse cell populations
  • End-to-end single-cell sequencing solution with simple, powerful data analysis

Applications and Uses

  • Assess cell-to-cell heterogeneity and identify new sub-populations
  • Map cell trajectories
  • Dissect transcriptional mechanics
  • Infer gene regulatory networks
  • Neurology research — normal brain function, neurological disease and psychological disorders
  • Immunology research — B Cell and T Cell subunit functional analyses
  • Cancer research — studies of cellular expansion of clonal cells in tumors and mutations that lead to differences in gene expression and drug response
  • Stem cell research — studies to better understand development and differentiation, including reverse engineering tissues

Included Components

  • ddSEQ Test Cartridges (12003862)
  • ddSEQ Cartridge Holder (12004739)
  • ddSEQ Single-Cell Isolator (12004336)
  • Power supply and power cord
  • User manual and product documentation

Related Products

Related Categories

Number Description Options
6855 Illumina® Bio-Rad® Single-Cell Sequencing Solution Brochure, Ver A Click to download
10000069430 ddSEQ™ Single-Cell Isolator Instruction Manual, Ver C Click to download
6863 Introducing the ddSEQ™ Single-Cell Isolator, SureCell™ WTA 3' Library Prep Kit, and SeqGeq™ Analysis Software Flier, Ver E Click to download