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.
Highlights
- 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
| Service | Sample type | Minimum amount | Minimum cell viability | Optimal 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 contact the core via email at [email protected] or call 713-500-7933 for more information.
Service workflow
Data analysis
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 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 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