Single-Cell RNA Sequencing

Explore cellular diversity at the single-cell level

The human body consists of more than 30 trillion cells. Within an organ or tissue, different cell types and cell populations occur. These cells are highly heterogenous regarding their transcriptional state. The cellular heterogeneity is an important feature of normal physiological processes. Different cell types and populations have different cellular functions, which are all required for the tissue’s or organ’s correct functioning. During disease progression, the composition of the different cell populations and their transcriptome may change or even contribute to the disease.

Traditional bulk RNA sequencing methods cannot resolve the heterogeneity of samples of different cell populations. However, single-cell RNA sequencing technologies now enable the analysis of individual transcriptomes from thousands of cells in a single sample. Thus, this technology can help resolve the transcriptional change on a cell type-specific level that may lead to the identification of new biomarkers or help further understand the biology of tissues or diseases.

Application areas of single-cell RNA sequencing:

  • detection of tumor heterogeneity
  • cell differentiation and lineage tracing
  • response to therapeutic interventions
  • biomarker discovery

We help you explore your samples’ cellular diversity by providing high-throughput 3‘ Single-Cell RNA Sequencing (3‘ SCR).

CeGaT Is the Best Partner for Sequencing Your Project


Scalable for different sample types, quantities, and requirements


Processing according
to highest quality

Customer Service

Constant scientific supervision of all
project steps

Made in Germany

In-house processing to maintain our reliable and trusted quality

Our Commitment to You

Fast Processing

Turnaround time
≤ 15 business days

High Quality

Highest accuracy for all processes

Secure Delivery

Secure provision of sequenced data via in-house servers

Safe Storage

Safe storage of samples and data after project completion

Our Service

We provide a comprehensive and first-class project support – from selecting the appropriate product to evaluating the data. Each project is supervised by a committed scientist. You will have a contact person throughout the whole project.

Our service includes:

  • detailed project consulting
  • product selection tailored to your project
  • detailed bioinformatic evaluation of your data
  • detailed project report with information about sample quality, sequencing parameters, bioinformatic analysis, and results

Benefit from our dedicated support and accredited workflows.

Explore Our Product for Single-Cell RNA Sequencing

We offer 3‘ Single-Cell RNA Sequencing (3‘ SCR) using the 10x Genomics® Chromium™ system and the latest NGS technology. Would you like to have bioinformatic analyses performed on your data in addition to the included deliverables? Each of our products can be supplemented with further services. We are happy to advise you.

3‘ SCR

Human, mouse
Other species might be possible upon request

Sample type
Frozen single cell suspensions

Sample requirements
1 million cells in 1 ml cryopreservation medium
> 90% cell viability
Other samples might be possible upon request

Chromium™ system (10x Genomics®)


Included deliverables
Project report & files in FASTQ format

If you are particularly interested in immune cells, please check our Single-Cell Immune Profiling portfolio.


Raw sequencing data are automatically processed. We offer different levels of bioinformatic analysis. The default level is Level 1. With increasing bioinformatic level, more data are delivered. All higher levels include the data from the lower levels. In addition to the data, and independent of the analysis level, a project report is generated.

We analyze your Single-Cell RNA Sequencing data with the Cell Ranger software from 10x Genomics®. This workflow includes read alignment, generation of feature-barcode matrices, cell clustering, and gene expression analysis.

Level 1:

  • demultiplexing of the sequencing data, including index reads (FASTQ format)

Level 2:

  • mapping of the sequencing data (BAM format)
  • standard Loupe Browser visualization file (CLOUPE format)
  • mapped count tables for downstream analysis (TSV format)
  • preliminary clustering analysis (CSV format)
  • preliminary differential gene expression analysis (CSV format)

Level 3:

  • For more than one sequenced sample, your Single-Cell RNA Sequencing data is combined into an experiment-wide matrix and reanalyzed after normalization.

Technical Information

We can process between 500 – 10,000 cells per sample, and up to 8 samples can be run in parallel on one Chromium Next GEM Chip. It is recommended to sequence at least 20,000 paired-end reads per cell. The required sequencing depth strongly depends on the sample type and on the experimental question.

At CeGaT, sequencing is performed using the Illumina sequencing platforms. If you require other sequencing parameters, please let us know! We can provide further solutions.

Our Workflow

Hier finden Sie den gesamten Prozessablauf

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Support & Offer

Support &

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Sample Receipt & Quality Control

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Library Preperation & Sequencing

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Bioinformatic Analysis & Data Delivery

Further Information about Single-Cell RNA Sequencing

To understand a system, you need to understand its components. If you look at complex biological systems, like the immune system or a growing tumor, understanding the function and behavior of the different cells in these systems is a big challenge. With single-cell RNA sequencing, scientist now have a great and powerful tool to face this challenge. In contrast to traditional bulk RNA sequencing, where gene expression levels are averaged across cells, single-cell RNA sequencing allows you to look at the gene expression of thousands of individual cells. Single-cell RNA sequencing is the perfect technique for all applications, where understanding cellular diversity is essential, like studying tumor heterogeneity, cellular differentiation, or therapy resistance.

At CeGaT, we provide high throughput single-cell RNA sequencing using the state-of-the-art Chromium system from 10x Genomics in combination with the latest NGS technology. The sample processing workflow includes three main steps: cell barcoding & library construction, sequencing, and data analysis. During cell barcoding, up to 10.000 single cells are encapsulated into tiny micro-droplets together with gel beads. These gel beads contain oligonucleotides with cell-specific barcodes and unique molecular identifiers. By labelling all mRNA molecules of a single cell with these two barcode sequences, their cellular origin is recorded, and each mRNA molecule can be uniquely quantified.

After cDNA synthesis and several library preparation steps, the samples are ready for sequencing. Sequencing is performed on one of our Illumina sequencers. Depending on the number of input cells and the read depth required per cell, we can adjust the sequencing output according to your needs. The generated sequencing data is then processed by our bioinformatic data analysis pipeline. During data analysis, the transcripts are quantified and assigned to the different cells. Cell clusters with similar gene expression patterns are identified and differential gene expression analysis between cell clusters is performed. Thus, you can identify different cell populations or cell phenotypes in your sample, and explore their function and behavior to enable you to fully understand the complexity of your sample.

Single-cell RNA sequencing, also known as scRNAseq, is a robust tool to detect rare cell populations in complex samples. It is well suited to determine cell type proportion shifts in time series experiments, where samples are collected over different time points. Single-cell RNA sequencing holds a great potential to discover new biomarkers and to analyze therapeutic mechanisms using differential gene expression or changes in cellular diversity on a cell-by-cell basis.

Video: Explore Cellular Diversity at Single-Cell Level


Singel-cell RNA Sequencing Flyer (EN)
Single-cell RNA Sequencing Tech Note (EN)
Single-Cell RNA Sequencing Description

Contact Us

Do you have a question or are you interested in our service? Feel free to contact us. We will take care of your request as soon as possible.

Start Your Project with Us

We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.

When getting in contact, please specify sample information including starting material, number of samples, preferred library preparation option, preferred sequencing depth and required bioinformatic analysis level, if possible.