High-Throughput Single-Cell Labeling with Indexing Droplets

inDrop is used for high-throughput single-cell labeling (Klein et al., 2015). This approach is similar to Drop-seq, but it uses hydrogel microspheres to introduce the oligonucleotides.

Single cells from a cell suspension are isolated into droplets containing lysis buffer. After cell lysis, cell droplets are fused with a hydrogel microsphere containing cell-specific barcodes and another droplet with enzymes for RT. Droplets from all the wells are pooled and subjected to isothermal reactions for RT. The barcodes anneal to poly(A)+ mRNAs and act as primers for reverse transcriptase. Now that each mRNA strand has cell-specific barcodes, the droplets are pooled and broken, and the cDNA is purified. The 3′ ends of the cDNA strands are ligated to adapters, amplified, annealed to indexed primers, and amplified further before sequencing.

Similar methods: CEL-Seq, Drop-seq, MARS-Seq, CytoSeq, Quartz-Seq, Hi-SCL


  • High-throughput, single-cell transcriptome profiling using a microfluidics system
  • Highly scalable to larger cell quantities
  • No fragmentation step


  • Low mRNA capture efficiency of ~7%
  • Droplets may contain 2 cells or 2 different types of barcodes


Illumina Library prep and Array Kit Selector


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