What Is Transcriptomics?
Transcriptomics is the study of the population of RNA molecules in biological samples that result from the balance of RNA production and RNA decay. It aims not only to count the number of RNA transcripts, but also the variety of RNA molecules that can result from a single transcript due to splicing, polyadenylation, 3’ to 5’ end-processing and other co- and post-transcriptional modifications, e.g. microRNAs.
Transcriptomics analyzes and interprets gene expression patterns under different conditions providing insights into functional genomics, regulatory mechanisms, and cellular functions.
Being one of the Four Big Omics, transcriptomics makes an indispensable contribution to the holistic view of biological systems. Its data are used in drug development, disease diagnosis and prognosis, personalized medicine, cancer research, neuroscience, agriculture, environmental monitoring to name a few.
Overcoming Challenges in Transcriptomics
While making breakthrough discoveries, researchers also encounter a variety of challenges. Here are a few of them:
- Difficulty in RNA extraction from specific biological samples
- Inaccurate detection of low-abundance transcripts
- Incomplete or biased data
- Inconsistent and unreliable analysis results
- Poor-quality and unstable RNA samples
- Human errors when performing multi-step protocols
- Labor-intensive and time-consuming techniques
- High-cost experiments
All these challenges can be largely overcome by automating transcriptomic protocols with trusted liquid handlers complemented with high-quality reagents and integrated instruments.
Our Automated Solutions for Transcriptomics
At Beckman Coulter Life Sciences, we have been dedicated to supporting transcriptomic studies since 1986 when we introduced the groundbreaking Biomek 1000 Automated Workstation. Today, our transcriptomic portfolio is renowned not only for advanced liquid handlers but also for outstanding integrations, easy-to-use software and SPRI bead-based genomic reagents. To provide you with seamless end-to-end transcriptomic solutions, we collaborate with our industry's most trusted companies.
The interactive workflow below is an example of how our solutions can be used in the most popular transcriptomic technique - RNA-Seq.
RNA Extraction Kits
Total Nucleic Acid Extraction Kits
Cleanup and Size Selection Reagents
Biomek i-Series Automated Workstations
Biomek NGeniuS Next Generation Library Prep System
Echo 525 Acoustic Liquid Handler
Biomek Echo One High-Throughput Genomics Bundled Solution
Integrated Workstations
RNA Extraction Kits
Total Nucleic Acid Extraction Kits
Cleanup and Size Selection Reagents
Biomek i-Series Automated Workstations
Biomek NGeniuS Next Generation Library Prep System
Echo 525 Acoustic Liquid Handler
Biomek Echo One High-Throughput Genomics Bundled Solution
Integrated Workstations
RNA Extraction Kits
Total Nucleic Acid Extraction Kits
Cleanup and Size Selection Reagents
Biomek i-Series Automated Workstations
Biomek NGeniuS Next Generation Library Prep System
Echo 525 Acoustic Liquid Handler
Biomek Echo One High-Throughput Genomics Bundled Solution
Integrated Workstations
RNA Extraction Kits
Total Nucleic Acid Extraction Kits
Cleanup and Size Selection Reagents
Biomek i-Series Automated Workstations
Biomek NGeniuS Next Generation Library Prep System
Echo 525 Acoustic Liquid Handler
Biomek Echo One High-Throughput Genomics Bundled Solution
Integrated Workstations
Benefits of Our Transcriptomic Solutions
Liquid Handling Solutions
- Biomek i-Series Workstations:
Pod Volume Inaccuracy CV Span-8 0.5 μL < 0.12% < 4.58% 900 μL < 0.102% < 0.392% MC-384 0.5 μL < 0.38% < 5.06% MC-96 950 μL < 0.1% <0.28% - Echo Acoustic Liquid Handlers enable users to transfer samples and reagents in volumes as small as 2.5 nL and can lower assay replicate requirements through increased assay precision.
- Biomek i-Series Workstations:
- Up to 45 deck positions and on-deck device utilization
- A range of pipetting head configurations: from a single Span‑8 pod to dual-multichannel heads (96/384).
- Echo Acoustic Liquid Handler allows for fast any-well-to-any-well transfers, enabling previously hours-long DNA/RNA normalization, barcoding, and pooling of libraries down to minutes-scale.
- Biomek Echo One High-Throughput Genomics Bundled Solution combines the power of acoustic miniaturization with the versatility of the Biomek workstation.
- Our experts have integrated 300+ different third-party devices from over 60 manufacturers to transform our liquid handlers into advanced lab automation solutions.
- Biomek i-Series Workstations can be integrated with LIM systems and can also be made to interface with AI tools and machine learning algorithms for data processing.
Reagents
- Powered by established high-performance SPRI technology, which uses paramagnetic beads to selectively bind nucleic acids by type and size.
- Ideal for RNA cleanup and extraction from cells, tissue, blood and even challenging formalin-fixed, paraffin-embedded (FFPE) samples.
- Library of demonstrated methods available for our lab automation solutions for nucleic acid extraction, cleanup and size selection for various throughput needs.
- Researchers have had successful extractions from small to large (HMW) nucleic acids from various sources as well as from a variety of different organisms, extracting both DNA and RNA from a single sample.
- You can use our chemistries with manual and/or fully automated methods on your choice of platforms, for optimum performance, flexibility and scalability.
Transcriptomic Workflows That We Automate
- mRNA-Seq
- Total RNA‑Seq
- RNA Exome Capture
- miRNA-Seq
- Targeted RNA‑Seq
- CITE-Seq
- Ribosome Profiling
- Size Selection
- NGS
- Miniaturization
- RNA Library Prep
- scRNA-Seq
- qRT-PCR
- Microarray
- Spatial Transcriptomics
- RNA-Seq
- DRUG-Seq
- Single-Cell Transcriptomics
- Whole Transcriptome Sequencing (WTS)
- RNA Extraction/ Cleanup
Single-Cell Transcriptomics
Single-cell transcriptomics explores high-resolution gene expression profiles in individual cells. Unlike the bulk transcriptome analysis, useful for understanding general gene expression trends of a population of cells, single-cell approaches help reveal unique transcriptional programs and identify rare cell populations and states.
Single-cell transcriptomics has revolutionized the fields of oncology, immunology, neuroscience, and beyond by offering a deeper understanding of cellular functions, interactions, and heterogeneity.
We have collaborated with 10X Genomics to streamline their single-cell transcriptomic application Chromium™ GEM-X Single Cell Gene Expression:
What Customers Are Saying
At Single Cell Discoveries the use of the Biomek i7 has supercharged our services workflow. By automating complex procedures, we have not only saved valuable time, but also minimized the risk of human error, ensuring consistently reliable data. Biomek i7 allows us to process large volumes of samples with remarkable speed and consistency, which is crucial for generating high-quality and reproducible data. Its flexibility and versatility enable us to customize protocols to meet the specific needs of our various transcriptomic applications. Moreover, the support from the Biomek team has been outstanding. They have provided us with comprehensive training and ongoing assistance, making sure we get the most out of the platform.
Oriol Llorà Batlle, Ph.D., Team Lead R&D, Single Cell Discoveries B.V.
Transcriptomics in Cancer Research
Transcriptomics plays a crucial role in cancer research by providing insights into spatiotemporal gene expression within cancer cells and tissues. This information is vital for understanding the molecular mechanisms driving cancer progression, metastasis, and treatment resistance.
Understanding genes and pathways that are dysregulated in cancer helps discover potential targets for new therapies. By comparing the transcriptomic profiles of cancerous and normal tissues, researchers can identify specific RNA molecules that can serve as biomarkers for early cancer detection, prognosis, and monitoring treatment response.
The main challenge in cancer research is the complexity and heterogeneity of cancer. Tumors are composed of a diverse mix of cell types, each with its own unique gene expression profile.
Spindle Cell Sarcoma Cytology
Our automation-friendly SPRI bead-based genomic reagents are indispensable for providing data reproducibility and reliability which are key to these studies in total and to identify rare cancer cell populations in particular. Among others, we offer reagent kits for extracting nucleic acids from one of the most commonly used sample types in cancer research – formalin-fixed paraffin-embedded (FFPE) tissue. For instance, our FormaPure XL Total kit allows you to extract DNA and RNA from the same sample without splitting it.
Extraction Kit
Featured Resources
Biomek i-Series Liquid Handlers
- Yao Z. et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 2021. doi: 10.1038/s41586-021-03500-8.
- Kind D. et al. Automation enables high-throughput and reproducible single-cell transcriptomics library preparation. SLAS Technol. 2022. doi: 10.1016/j.slast.2021.10.018.
- Santacruz D. et al. Automation of high-throughput mRNA-seq library preparation: a robust, hands-free and time efficient methodology. SLAS Discov. 2022. doi: 10.1016/j.slasd.2022.01.002.
Echo Acoustic Liquid Handlers
- Mayday M.Y. et al. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. PLoS ONE. 2019. doi: 10.1371/journal.pone.0206194.
- Ye C. et al. DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery. Nat Commun. 2018. doi: 10.1038/s41467-018-06500-x.
- Larman H.B. et al. Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay. Nucleic Acids Res. 2014. doi: 10.1093/nar/gku636.
- Harrill J.A. et al. High-Throughput Transcriptomics Platform for Screening Environmental Chemicals. Toxicol Sci. 2021. doi: 10.1093/toxsci/kfab009.
- Li J. et al. DRUG-seq Provides Unbiased Biological Activity Readouts for Neuroscience Drug Discovery. ACS Chem Biol. 2022. doi: 10.1021/acschembio.1c00920.
- Thomas J.R. et al. Enhancing the Small-Scale Screenable Biological Space beyond Known Chemogenomics Libraries with Gray Chemical Matter─Compounds with Novel Mechanisms from High-Throughput Screening Profiles. ACS Chem Biol. 2024. doi: 10.1021/acschembio.3c00737.
- Bush E.C. et al. PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens. Nat Commun. 2017. doi: 10.1038/s41467-017-00136-z.
- Huot L. et al. Spodoptera frugiperda transcriptional response to infestation by Steinernema carpocapsae. Sci Rep. 2019. doi: 10.1038/s41598-019-49410-8.
- Isobe Y. et al. Manumycin polyketides act as molecular glues between UBR7 and P53. Nat Chem Biol. 2020. doi: 10.1038/s41589-020-0557-2.
Genomic Reagents
- Finseth F.R. and Harrison R.G. A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird. PLoS One. 2014 . doi: 0.1371/journal.pone.0108550.
- Callari M. et al. In-depth characterization of breast cancer tumor-promoting cell transcriptome by RNA sequencing and microarrays. Oncotarget. 2016. doi: 10.18632/oncotarget.5810.
- Zhang Z. et al. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease. Cell Rep Methods. 2023. doi: 10.1016/j.crmeth.2023.100395.
- Haile S. et al. Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis. PLoS One. 2017. doi: 10.1371/journal.pone.0178706.
- Gharaie S. et al. Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys. Sci Rep. 2023. doi: 10.1038/s41598-023-48213-2.
- Gaisser K.D. et al. High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding. Nat Protoc. 2024. doi: 10.1038/s41596-024-01007-w.
- Zou S. et al. Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer. J Transl Med. 2024. doi: 10.1186/s12967-024-04984-4.
- Alfonso-Gonzalez C. et al. Identification of regulatory links between transcription and RNA processing with long-read sequencing. STAR Protoc. 2023. doi: 10.1016/j.xpro.2023.102505.
- Pérez-Mojica J.E. et al. Continuous transcriptome analysis reveals novel patterns of early gene expression in Drosophila embryos. Cell Genom. 2023. doi: 10.1016/j.xgen.2023.100265.
Our Transcriptomics Partners
Not intended or validated for use in the diagnosis of disease or other conditions.
ECHO is a trademark or registered trademark of Labcyte Inc. in the United States and other countries. Labcyte is a Beckman Coulter company.
© 2000-2025 贝克曼库尔特国际贸易（上海）有限公司保留最终解释权
NOT ALL PRODUCTS ARE AVAILABLE IN ALL COUNTRIES.
PRODUCT AVAILABILITY AND REGULATORY STATUS DEPENDS ON COUNTRY REGISTRATION PER APPLICABLE REGULATIONS
The listed regulatory status for products correspond to one of the below:
IVD: In Vitro Diagnostic Products. These products are labeled "For In Vitro Diagnostic Use."
ASR: Analyte Specific Reagents. These reagents are labeled "Analyte Specific Reagents. Analytical and performance characteristics are not established."
CE: Products intended for in vitro diagnostic use and conforming to European Directive (98/79/EC). (Note: Devices may be CE marked to other directives than (98/79/EC)
RUO: Research Use Only. These products are labeled "For Research Use Only. Not for use in diagnostic procedures."
LUO: Laboratory Use Only. These products are labeled "For Laboratory Use Only."
No Regulatory Status: Non-Medical Device or non-regulated articles. Not for use in diagnostic or therapeutic procedures.
沪ICP备18036651号-1
沪公网安备 31010502004935号
互联网药品信息服务资格证书（沪）-非经营性-2020-0189
沪(浦)应急管危经许[2022]200234