Cancer Genomics Center

Flex scRNAseq (single-cell RNAseq using fixed cells)

Single-cell RNA sequencing is becoming increasingly utilized for profiling larger sample numbers, such as cohorts of patients or diverse perturbations. Establishing an efficient and scalable workflow is crucial in this context. Paraformaldehyde (PFA) fixation enables the collection, shipment, and analysis of samples to a central location without compromising integrity or data quality. This opens up new possibilities for sample accessibility, throughput, and batched analysis. Furthermore, advanced chemistry extends single-cell transcriptomic profiling to formalin-fixed, paraffin-embedded (FFPE) tissue, broadening the range of accessible sample types. With a scalable workflow, it is now possible to profile up to a million fixed single cells simultaneously, allowing for flexibility in scheduling while meeting the specific needs of translational and clinical labs dealing with fragile samples or time constraints that would otherwise impede analysis.

Highlights

• Preserve biological states and fragile cells by fixing fresh samples at the collection point.
• Enhance the efficiency of single-cell workflows through improved sample collection, preparation, and processing steps.
• Streamline processes and increase efficiency by batching and multiplexing samples, thereby minimizing experimental variability.
• Achieve large-scale and highly sensitive measurements of gene expression.
• Unlock new possibilities in single-cell analysis by gaining access to archived samples.

Sample submission requirements

Service	Sample Type	Minimum Amount	Morphology	Debris
Flex scRNAseq	Single cells or Single nuclei	100,000	Intact membrane	low

• Single cells/single nuclei are suspended in frozen media and sent on dry ice
• The cells/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 (cgc@uth.tmc.edu or 713-500-7933) for the detail information.

Service Workflow

 

Fixed RNA Profiling with Cell Ranger multi

Cell Ranger v7.0 and later supports analyzing Fixed RNA Profiling (FRP) data with the cellranger multi pipeline (see library compatibility table). FRP data cannot be analyzed with the cellranger count pipeline. Please follow the instructions of the link.

Useful documents

• Chromium Fixed RNA Profiling User Guide for Multiplexed Samples (CG000527)
• Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling (CG000478)
• Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling (CG000553)
• Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling (CG000632)
• Probe set: Human (18,532 genes targeted by 53,957 probes) and Mouse (19,405 genes targeted by 55,479 probes).
• Flex scRNAseq Tested Tissues.
• Comparison among Flex scRNAseq, scRNAseq (3’ assay), and Single Cell Immune Profiling (5’ assay)