Gene Expression & Proteomics Analysis

To study and comprehend the true impact of drugs requires not only the measurement of changes in gene expression caused by a drug (transcriptomics), but also the output of these expression changes seen in protein expression (proteomics) that ultimately relate to tumor cell killing.



Due to the dynamic nature of tumors and their infiltrating lymphocytes, it is important to look beyond genetic variation to assess the phenotypic changes in protein and gene expression levels that are a result of drug challenge in order to fully characterize the immune response to disease.

Nilogen’s 3D-EXplore platform’s portfolio of gene expression services include bulk RNA sequencing, NanoString and single-cell RNA sequencing, combined with CITE-seq protein expression analysis. These analyses allow for a side-by-side multiplexed analysis of multiple drug challenges in the same fresh patient tumor sample. Sorting and analysis of cells from fresh rather than previously frozen materials prevent the loss of rare cells and protein expression by 60% or more. With this approach we can analyze drug mediated changes in the TME and help develop biomarkers of response that can be valuable in drug development and clinical studies.


NanoString Gene Expression Analysis

We provide the complete range of NanoString nCounter panels to study the biology of tumors, providing a fast and high-throughput multiplexed gene expression analysis of the response to therapeutic intervention in fresh patient tumors.

Single Cell RNA Sequencing

Enables the quantitative measurement of the molecular activity that underlies the phenotypic diversity of cells within a tumor by sequencing individual cells. Intra-tumor heterogeneity is common across all tumor types. Accurate characterization of this heterogeneity is essential for determining the mechanisms of cancer pathogenesis and identification of novel targets for immunotherapy and drug development.


TOTALSeq works hand-in-hand with scRNAseq to enable the simultaneous measurement of protein and RNA at the single cell level, providing enhanced cell type identification. Evaluate the impact of drug therapy on up to 130 protein markers in conjunction with the transcriptome of each cell; this enables the single cell analysis of individual immune cells in a heterogeneous tumor microenvironment.

Scientific Data


Gene Expression Profiling Services in combination with TOTALSeq protein expression enables a granularity of single cell phenotypic analysis that has been previously unachievable.

Related Resources

Browse our latest posters and presentations using Nilogen's fresh patient tumoroid technology.


Contact Us to Discuss Your Project requirements