Technical Support and Resources
Explore the latest support resources and FAQs for SimpleCell 3′ Gene Expression kits or reach out to the support team for more information about your project.

SimpleCell Knowledge Base
Access SimpleCell 3′ Gene Expression site prep, workflow, and troubleshooting documentation on the CS Genetics Knowledge Base.
SimpleCell Frequently Asked Questions
What is the SimpleCell 3' Gene Expression Kit used for?
The SimpleCell 3′ Gene Expression Kit is designed to quantify gene expression at the 3′ end of mRNA transcripts. It provides a cost-effective, streamlined solution for transcriptome analysis, making it ideal for high-throughput studies such as population-scale profiling, drug-screening, and translational discovery
What sample types are compatible with this kit?
The kit is compatible with a wide variety of tissues and cell types including cultured cells, primary cells, organoids, and dissociated solid tissues.
How many cells are required for input for the assay?
Typical input requirements range from 5,000-8,500 cells, though as little as 1,000 cells may be used for each sample. In some cases, higher cell inputs can be used to increase output. For questions, please refer to the Cell Input Requirements section of our support page.
Does this kit support Organoids?
Yes, the SimpleCell kit is optimized for use with dissociated organoids. Please refer to the Cell Input Requirements section of our support page for input recommendations.
What sequencing platforms are supported?
The library prep workflow produces Illumina-compatible sequencing libraries. It can be used with common Illumina instruments including NovaSeq, NextSeq, and MiSeq platforms.
Other sequencing platforms may be used (Element AVITI and Oxford Nanopore Technologies). Please refer to sequencing provider websites for recommendations on converting libraries.
How many reads per cell are recommended for SimpleCell?
30,000 reads/cell is the recommended sequencing depth for SimpleCell.
What is the turnaround time for library preparation?
Library preparation can typically be completed in under 8 hours.
How many samples can I multiplex?
Sample multiplexing is achieved by using unique dual indexed sequencing adapters. The number of samples that you can multiplex into a single sequencing pool is determined by your desired sequencing depth and the number of UDIs to which you have access. We can supply up to 96 UDIs in our Accessory Starter Kits or you can purchase them from your supplier of choice. For more information or to multiplex more samples, please contact Technical Support
Is there a recommended bioinformatics pipeline?
Yes, CS Genetics provides a streamlined, open-source pipeline to process your sequencing outputs. It includes quality control, alignment, deduplication, and a QC report. Compatibility with open-source tools like STAR and Salmon is also supported. You can access the pipeline here: CS Genetics scRNA-seq Pipeline on GitHub
What kind of data output should I expect?
The kit generates 3′ reads for single-cell analysis. The output will be a count matrix file which is compatible with ScanPy or Seurat for downstream analysis.
Where can I get technical support or reorder the kit?
You can reach our technical support team via support@csgenetics.com. To reorder the kit or request a quote, visit our Products page or contact your CS Genetics representative.
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