Platforms

10X Genomics Chromium

The 10X Genomics Chromium Controller is a single-cell profiling technology that enables the analysis of large cell numbers at a high capture efficiency (of up to 65%). The platform allows for high-throughput single cell transcriptome, immunome, or copy number analysis in a variety of cell types as well as single-cell nuclei. The flexible workflow encapsulates up to 10,000 cells or nuclei per sample together with gel beads into nanodroplets (single-Poisson distribution loading). Up to eight samples can be processed per run allowing for capture of up to 80,000 cells per run. Trained core staff will prepare the libraries from single-cell suspensions submitted by the research investigator. Cells can be suspended in a wide range of media or buffers. Please see the 10X Sample Prep Guidelines for recommendations.

  • Cell Viability needs to be >90%
  • Cell concentration needs to be 750-1200 cells/µl and should be determined via an automated counter. If you do not have access to one, please talk to the VUMC Flow Core. The resulting data are analyzed with the free Cell Ranger and Loupe Cell Browser software.

 

Bio-Rad ddSEQ

The Bio-Rad ddSEQ is a ‘droplet’ based single-cell processing technology that is coupled with Illumina library prep reagents to allow for Single-Cell RNA-sequencing. The ddSEQ instrument captures single cells on a smaller scale than the 10X Chromium. Each chip contains four partitions, which can be loaded with the same or unique samples. Each partition can capture up to 400 cells, enabling capture of ~1,600 cells on a single run. As with the 10X system, trained core staff will prepare the libraries from single-cell suspensions submitted by the research investigator. Cells should be in suspended in cold PBS with 0.1% BSA.

  • Cell Viability needs to be >95%
  • Cell concentration needs to be 2250-2750 cells cells/µml and determined by an automated cell counter.

 

The resulting data are analyzed with SureCell RNA Single-Cell application available in Illumina’s BaseSpace Sequence Hub.