High-Throughput Gene Expression Screening


High-throughput gene expression (HT-GEx) screening is an RNA-Seq-derived approach we developed for optimal drug discovery and analysis, similar to DRUG-Seq. Unlike microarrays, our method offers rapid, unbiased, 3' gene expression screening, providing complete cell-to-data analysis of the transcriptome at a lower cost than standard RNA sequencing. Working directly from lysate, GENEWIZ High-Throughput Gene Expression Screening works directly from cell lysate, saving both time and money by removing the need for RNA purifications. Additionally, the method performs 3’ transcript tagging to reduce required sequencing depths.



Engineering the Future: Unlocking the Potential of
Functional RNAs in Biology, Medicine, and Innovation

Thursday, July 25, 2024 | 11:00AM EDT


High-Throughput Gene Expression Screening Applications

Drug Discovery

Compound Treatment Phenotyping

CRISPR Treatment Phenotyping

Cell Response Screening



High-Throughput Gene Expression Screening Assay Comparison

Metric HT-GEx Screening mRNA-Seq Total RNA-Seq Iso-Seq
 Reads/Sample  ~1-2M Reads  ~10-30M Reads ~20-45M Reads  ~1-2M Reads 
 Min. Sample Size  96/384  1  1
Cost  $ $$  $$$   $$$$
 Starting Material  Cell Lysate >20ng Total RNA   >100ng Total RNA >1ug Total RNA 
 Selection Method  Poly(A) +   Poly(A) +  rRNA -   Poly(A) +
 Detection Level  3' Tails of Genes  Poly(A) Transcript All Transcript   Full-Length Poly(A) Transcript
Gene Expression

Variant Detection

Alternative Splicing
 Transcriptome Assembly

Suitable method | Preferred method | Not a suitable method

High-Throughput Gene Expression Screening Deliverables


Standard Deliverables

  • FASTQ files
  • Quality summary report

Advanced Analysis

(In addition to standard deliverables)

  • UMI extraction, mapping, counting, and transformation
  • Normalization
  • Differential gene expression and clustering by compound/treatment

Custom bioinformatics analysis and reports are available. Please contact us about how we can customize the analysis to answer your biological question.

High-Throughput Gene Expression Screening Features & Benefits

Digital Spatial Profiling Stains

Fast Turnaround Times

Starting at just 2 weeks for quick target discovery

Digital Spatial Profiling Target Areas

High-Throughput Capacity

To rapidly scale up pilot or discovery projects

Photocleave Barcodes

Superior Data Quality

Exceeding manufacturers’ benchmarks

High-throughput, cell-to-data solution for compound screening

Low-cost, unbiased coverage for use in selection of drug candidates

Receive detailed expression data for each well across multiple 96- or 384-well plates

Free technical consultation and customer support from Ph.D.-level project managers and lab scientists

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Webinar Series | Advancing Transcriptomics: Gene Expression Screening, Single-Cell RNA-Seq, and Beyond

With this two-part webinar series, go beyond traditional transcriptomics and learn about the various NGS approaches available for gene expression analysis. In part 1, we take an in-depth look at various gene expression approaches, including RNA-Seq, single-cell RNA-Seq, digital spatial profiling, and more. In part 2, we explore the data generated from these approaches and how they can complement each other and confirm findings.

High-Plex Spatial Analysis of Tissue Microenvironments

Tech Note | Achieving Phenotypic Profiling for Rapid Drug Discovery with High-Throughput Gene Expression Screening

High-throughput technologies are critical in performing phenotypic profiling for drug discovery applications. In this tech note, Azenta Life Sciences discusses the challenges associated with traditional approaches, such as microarrays and RNA sequencing, and offers an optimized assay to achieve high-quality phenotypic profiling at a reduced cost for rapid drug discovery.

High-Plex Spatial Analysis of Tissue Microenvironments

Information Sheet | High-Throughput Gene Expression (HT-GEx) Screening

Download our information sheet for a brief overview of Azenta Life Scences' high-throughput gene expression screening service.                                         



For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing-only projects.

10x Genomics

How To Order

Email | Phone 1-877-436-3949, Ext. 1