Multiomics and single-cell analysis

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Individualized technologies enable the readout of high-quality, molecular information from single cells.

Single-cell sequencing provides high-resolution glimpses into cellular heterogeneity and interactions between different cell types. It allows a high number of cells to be analyzed, making it a powerful tool for characterizing rare cell types and different cell states (cell plasticity). It is therefore possible to trace the consequences of local cell dysfunctions and to directly identify changes that occur in pathological situations (in autoimmune diseases, chronic diseases, or cancer).

The response and progression of diseases during therapy can be identified in particular through high-resolution determination of the change in cellular heterogeneity in liquid biopsies — and also through the individual change in single cells, such as circulating tumor cells.


  • Individualized technologies enable the readout of high-quality, molecular information from single cells.
  • Miniaturization and automation allow high-throughput analysis to be provided at a reduced cost.
  • Long-read technologies make it possible to characterize complex genomic regions or transcript isoforms and to determine base modifications.

Our Services

Single-cell DNA analysis

The first step in the molecular characterization of single-cell genomes is genome amplification using Ampli1 Whole Genome Amplification (WGA).

The miniaturization and automation of the method allow high-throughput analysis to be provided at a reduced cost. Our established three-step quality control process also enables samples to be identified reliably and with sufficient quality for downstream NGS analysis.

Single cell transcriptomic analysis

3' or 5' RNA sequencing using 10X microfluidic genomics technology

Application: This method is useful when the number of available cells is high and the objective of the study is to identify cell types based on common expression profile patterns or to combine the method with other technologies, such as ATAC-Seq or feature barcoding for Multiomics applications.

Transcriptomic sequencing of single cells using the Smart-Seq2 method

Application: The Smart-Seq2 protocol is both automated and miniaturized, making it cost-effective to use for a small to medium number of cells. Three-step quality control after whole transcriptome amplification makes the selection of high quality cells for NGS analyses possible. Smart-Seq2 generates full-length transcriptomes, which, besides differential expression analysis, allows for the identification of point mutations and quantification of isoforms.

Single-cell RNA-Seq using Ampli1 Whole Transcriptome Amplification (WTA)

Application: This method also generates full-length transcripts and can be combined with Ampli1 WGA to analyze the genome and transcriptome of the same single cell.

Long-read sequencing

At Fraunhofer ITEM, we have a PromethION and a MinION Oxford nanopore sequencer. Unlike Illumina sequencing, ONT sequencing generates very long reads that are limited only by the length of the input material. We therefore have established methods for isolating high molecular weight DNA.


  • Investigating difficult genomic regions, especially complex structural variants and complex aberrations
  • Detecting the methylation status of sequenced DNA without further modification of the library preparation 
  • Direct RNA sequencing for differential transcriptional analysis, isoform detection, and epitranscriptomics 

miRNA sequencing

At Fraunhofer ITEM, we have developed a method that enables the sequencing of small, non-coding RNAs — particularly microRNAs (miRNAs) — from single cells. Our miRNA-Seq method provides sensitive and reproducible results with cell lines from various tissues of origin, circulating tumor cells from the blood of cancer patients, and even single cells from cryopreserved tissue that has been dissociated to form a single-cell suspension after thawing. Spike-ins are available as an internal quality control. The miRNA-Seq method is both automated and miniaturized and can be performed in both 96 and 384-well formats.


Stefan Kirsch

Contact Press / Media

Dr. Stefan Kirsch

Manager of the Working Group on Innovative Molecular Technologies and Biomarker Discovery

Christopher Jakobs

Contact Press / Media

Dr. Christopher Jakobs

Business Development for Personalized Tumor Therapy

Phone +49 152 28220636