Skip Navigation and Go To Content

Cancer Genomics Center


scRNAseq (Single-cell RNA sequencing, 10x Genomics 3’ kit)

The Chromium Single Cell Gene Expression Solution provides a scalable microfluidic platform for gene expression profiling of 500-10,000 individual cells per sample. A pool of ~3,500,000 10x Barcodes are sampled separately to index each cell’s transcriptome. It is done by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNA shares a common 10x Barcode. Dual indexed libraries are generated and sequenced from the cDNA and 10x Barcodes are used to associate individual reads back to the individual partitions.

Photo of scRNAseq Single-cell RNA sequencing 10x Genomics 3 kit


  • Analyze how cellular heterogeneity contributes to your biological system with transcriptional profiling at single cell resolution across tens of thousands of cells
  • Gain new insights into cell subtypes and states with multiomic readouts of gene and cell surface protein expression
  • Explore cellular phenotypes with whole transcriptome analysis
  • Investigate complex genetic networks and perturbed transcriptomes in normal and diseased cell types by simultaneously detecting CRISPR guides and single cell gene expression profiles

Sample Submission requirements

ServiceSample typeMinimum amountMinimum cell viabilityOptimal concentration
scRNA Immune Single cells 50,000 85% 700-1200 cells/ul

  • Single cells are suspended in 1xPBS with 0.04%BSA
  • Samples have to be sent to core before 1 PM
  • The nuclei will be checked the quality and the core has the rights to determine if the samples are qualified for the experiment
  • Please check the core or 713-500-7933 for the detail information.

Service workflow

Photo Service Workflow Diagram scRNA-seq

Data analysis

Cell Ranger

Cell Ranger is a set of analysis pipelines that processes Chromium Single Gene Expression data to align reads, generate Feature Barcode matrices and perform clustering and gene expression analysis.

  • Input: Base call (BCL) and FASTQ
  • Output: BAM, MEX, CSV, HDF5, Web Summary, .cloupe/.loupe
  • Operating System: Linux
Cloud Analysis

Cloud Analysis is currently only available for US customers. Cloud Analysis allows users to run Cell Ranger analysis pipelines from a web browser while computation is handled in the cloud.

  • Key features: scalable, highly secure, simple to set up and run
  • Input: FASTQ
  • Output: BAM, MEX, CSV, HDF5, Web Summary, .cloupe/.loupe.

Loupe Browser

Loupe Browser is an interactive data visualization tool that requires no prior programming knowledge.

  • Input: .cloupe
  • Output: Data visualization, including t-SNE and UMAP projections, custom clusters, differentially expressed genes
  • Operating System: MacOS, Windows

Useful documents