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Single cell RNA-Seq (scRNA Seq) is a tool that enables simple and robust access to the transcriptomes of thousands of single cells – giving unprecedented insight into tissues at single cell resolution. This offers vital information about heterogeneity and cell-specific dynamics, which is key to understanding many diseases, immunity, development and more.

This is in contrast to traditional techniques, that either allowed analysis of a few genes in thousands of individual cells (e.g., in situ hybridization), or the expression profile of thousands of genes, but only on a tissue homogenate.

Research Areas

  • Cardiovascular
  • Plants
  • Immunology
  • 3D Cell Culture
  • Long Read Sequencing

What is the drop-seq method?

The drop-seq method was originally developed by Macosko et al. in 2015 and has since emerged to one of the most popular single cell RNA-Sequencing (scRNA-Seq) methodologies.

Core Principles of Drop-Seq

  • Encapsulation of single cells with barcoded mRNA-capture beads
  • The use of a microfluidic device/chip to create nanoliter-scale aqueous droplets formed by precisely combining aqueous and oil flows
  • The use of molecular barcoding beads to distinguish the cell-of-origin of each mRNA
  • Reverse transcription added post encapsulation using a template switching oligo

The methodology involves encapsulating single cells with single barcoded mRNA-capture beads in nanoliter-sized droplets. Beads are suspended in lysis buffer that upon encapsulation with cells inside a droplet, break open the cell and thereby releases the mRNA.

The barcoded oligo bead library is constructed such that each bead has a unique DNA barcode sequence, but within a bead, the thousands of copies of oligo all contain an identical barcode sequence. The 3′ end of the oligo has a poly(dT) stretch that captures mRNA and primes reverse transcription.

Subsequently, beads are then released from their droplets and subjected to reverse transcription. The cDNA product is a full-length amplicon of the mRNA transcript due to the use of template switching oligonucleotide. Further on, the cDNA is amplified and sequenced using conventional library preparation methods and Next Generation Sequencing such as offered by Illumina, PacBio or Oxford Nanopore Technologies.



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