Genomics for Statisticians 3: Small- and large-scale single-cell sequencing

Genomics

We overview single-cell RNA sequencing, at both small and large scales.


Author

Affiliation

Tim Barry

 

Published

Aug. 15, 2022

DOI


1. Single-cell sequencing

Single-cell sequencing is a technology that provides a snapshot of the transcriptome (i.e., the set of gene expressions) of a collection of individual cells. We present a brief ovewview of single-cell sequencing.


The oligo is made of up several smaller parts.

  1. PCR handle – this is required for the PCR and sequencing steps; it is common across all oligos on all beads.
  2. Cell barcode – this identifes the cell; importantly, the cell barcode is the same across all oligos on a given bead.
  3. UMI (unique molecular identifier) – each oligo on a given bead has a distinct UMI. The UMI eliminates bias that arises during the PCR and sequencing steps.
  4. Poly-dt sequece – a long sequence of T nucleotides. This captures the mRNA transcripts, which are polyadenylated after transcription.

2. Large-scale single-cell sequencing



3. Applications