10X Genomics Single-Cell Analysis

Single-cell sequencing is changing our understanding of fundamental biological processes such as development, immunity, pathology, and disease. Single-cell analysis is now necessary for any research aimed at examining cell populations, their distinct genomic composition, and their responses to treatment. Thus, a better and more automated system is an urgent need for investigators at UTHSA.

10X Genomics Chromium platform, application-specific sequencing preparation kits, with GSF’s variety of Illumina platforms (NovaSeq and NextSeq), and their analysis software, provide users with the latest and most advanced high-throughput sequencing technology available for single-cell genomics with a fully integrated solution. This new and promising technology enables the generation of excellent genomic data: (1) The Chromium Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells. The latest improvements allow you to detect even more unique transcripts per cell and with the addition of Feature Barcoding technology, you can get a more complete molecular readout cell by cell—identify cell-specific CRISPR-mediated perturbations or simultaneously measure gene and cell surface protein expression in the same cell, with virtually unlimited possibilities for the additional feature types. (2) The Chromium Single Cell Multiome ATAC and Gene Expression: Simultaneously profile gene expression and open chromatin from the same cell. (3) The Chromium Single-Cell Immune Profiling Solution is a comprehensive approach to simultaneously examining the cellular context of the adaptive immune response and immune repertoires of hundreds to tens of thousands of T and B cells in humans or mice on a cell-by-cell basis.

The GSF performs single-cell analysis through a 10X Genomics Chromium system.   For 10X Genomics single-cell studies, the GSF provides the library preparation and sequencing for the following applications:

  • Single-cell RNA-seq: Provide 3’ digital gene expression by profiling 500 to 10,000 individual cells per sample
  • Single-cell Multiome ATAC and Gene Expression: Simultaneously profile gene expression and open chromatin from the same cell
  • Single-cell Immune Profiling: Sequence VDJ and TCR regions while assessing the gene expression profiles of immune cells
  • More applications will follow from the updates of 10X Genomics new products

Some facts you like to know before getting started on the single-cell project:

  • 10x Genomics’ single-cell RNA-seq (scRNA-seq) technology, the Chromium™ Single Cell 3’ Solution, allows you to analyze transcriptomes on a cell-by-cell basis through the use of microfluidic partitioning to capture single cells and prepare barcoded, next-generation sequencing (NGS) cDNA libraries. Specifically, single cells, reverse transcription (RT) reagents, gel Beads containing barcoded oligonucleotides, and oil are combined on a microfluidic chip to form reaction vesicles called Gel Beads in Emulsion, or GEMs. GEMs are formed in parallel within the microfluidic channels of the chip, allowing the user to process 100’s 10,000s of single cells in a single 18-minute Chromium™ Instrument run (V3.1). It’s important to note that cells are loaded at a limiting dilution in order to maximize the number of GEMs containing a single cell to ensure a low doublet rate while maintaining a high cell recovery rate of up to ~65%.
  • Cell density and viability are important! The optimal cell density of your single-cell suspension stock is 1000 cells/ul, and viability > 90%.
  • Please note: 10X single cell service is by appointment only; we must have advance notice (1-2 weeks preferred) due to the nature of these preparations since we will need to have someone on standby to receive the cells. Please read 10x Genomics GSF Recommendations before you prepare/submit your samples to the GSF.
  • Please check these presentations if you are interested in this technology, sample preparation, and data analysis.
  • How many cells do we need to sample so that we see at least n cells of each type?  https://satijalab.org/howmanycells/

If you are interested in working with the GSF for the single-cell experiment, please read Submission of Samples.

Inquire About Our Services:

The Genome Sequencing Facility Provides genomic service of Illumina next-generation sequencing and single-cell analysis using 10X Genomics for researchers, both inside and outside of UT Health San Antonio, other academic institutions, and the biotechnology and pharmaceutical industries.

Zhao Lai, PhD
Director, Genome Sequencing Facility
Greehey CCRI
UT Health San Antonio
8403 Floyd Curl Dr.
San Antonio, TX, 78229, USA
Office: GCCRI 4.100.14
Phone: (210) 562-9246