GENOME TECHNOLOGY ACCESS CENTER • DEPARTMENT OF GENETICS • WASHINGTON UNIVERSITY SCHOOL OF MEDICINE

Single Cell RNA-seq

GTAC offers two formats of single-cell RNA-seq:

  • Chromium Single Cell 3′ Solution from 10X Genomics
    • Appropriate for 100s to 10s of 1000s of cells
    • All cDNA from each cell receives a unique molecular barcode which allows libraries from many cells to be sequenced together.
    • GTAC uses either the Illumina HiSeq2500 or NovaSeq6000, depending on the depth of sequencing required.
    • Chromium Software Suite for 10X provides analysis and visualization. In addition to our analysis, the software is available at no charge.
  • GTAC also offers sequencing of plated single cells, typically achieved with a FACS sorter (FACS-seq)
    • Appropriate for smaller populations: 100-300 cells
    • All cDNA from each cell receives a unique molecular barcode which allows libraries from many cells to be sequenced together.
    • GTAC uses either the Illumina HiSeq2500 or NovaSeq6000, depending on the depth of sequencing required.
    • RaceID_ET & Seurat informatics analysis

Current methods for quantifying molecular states of cells usually depend on measuring the mean gene expression values from hundreds to millions of cells. Given the heterogeneity of cell populations, these mean values miss differences and, perhaps, interactions within a cell population. RNA with low copy number, which may exert important functions, is usually undetectable or regarded as noise in these bulk cell-averaging methods.

By combining a variety of small-volume library prep methods and next generation sequencing (NGS), single-cell RNA sequencing (scRNA-seq) provides the RNA expression profile of individual cells. scRNA-seq can identify rare cell types within a cell population, creating and tracking sub-population structures. Uncommon transcripts, which are obscured in bulk sequencing can be revealed. Even genetically identical cells, under the same environment, can display variability of gene expression levels.

The Genome Technology Access Center now offers two different scRNA-seq platforms: FACS-seq for relatively small homogenous populations, and emulsion library prep, using the Chromium Single Cell 3′ Solution from 10X for more heterogeneous larger pools.

In addition to the generation of raw data, GTAC offers analysis at no additional charge. These include raw and normalized gene counts, statistical comparisons, clustering and pathway analysis. We have scRNA-seq-dedicated pipelines for both formats. Data samples can be provided by request.