Cancer cell line models have been a cornerstone of cancer research for decades. Profiling cancer cell lines can be a powerful tool to identify gene alterations or cancer-related pathways and aid in discovering putative drug targets. In this webinar, we'll use QIAGEN OmicSoft Lands and QIAGEN Ingenuity Pathway Analysis (IPA) to help you select cell lines and translate insights from your cell line experiments for drug target discovery.
During this 90-minute discussion, we'll explore how you can use these software tools to:
• Select appropriate cancer cell lines for a variety of applications such as drug discovery, precision disease modeling, understanding gene function in cancer, immune-oncology research and more
• Examine various 'omics data for genes of interest for expression, mutation, hotspots and gene dependency data
• Generate networks for hypotheses and test them in silico to improve the translation of insights derived from cell line models to the drug target identification
• Integrate analyses of public 'omics data and drug response phenotypes using cell line model systems by exploring data from the Library of Integrated Network-Based Cellular Signatures (LINCS)
• Prioritize drug targets and profile phenotypic/downstream effects of drug action by overlaying public data on user-generated networks
Our system uses millions of curated literature findings from QIAGEN Knowledge Base and the OmicSoft digital warehouse. This discussion is intended for both those familiar with QIAGEN IPA and newcomers interested in learning more.
What powerful partnerships come to mind when you think of great collaborations? The two big Steves (Jobs and Wozniak) who became digital giants? The unstoppable Williams sisters who teamed up on the tennis court to win 4 Grand Slam tournaments and three Olympic golds? Marie and Pierre Curie, one of the greatest science duos of all time, who discovered radioactivity?
Their inspirational legacies leave us all in awe and remind us of the magic and impact of combining two strong and innovative forces.
We've got another exciting partnership to share with you, and if you're a preclinical researcher, prepare to be thrilled. Our recent collaboration with ATCC combines our strength of collecting, integrating and manually curating high-quality 'omics data with ATCC's authenticated, traceable and highly trusted cell lines. The result? A powerful tool that the drug development industry can't afford to ignore.
Because as a preclinical researcher, you know choosing the right cell lines for your studies is crucial. Yet the selection process is often challenging due to the lack of access to genomic profiles before purchasing cell lines. Our new tool—ATCC Cell Line Land, which was born from our partnership with ATCC—revolutionizes cell line selection by providing authenticated cell line 'omics data.
So, let's explore what's so great about this partnership and how authenticated cell line ‘omics data will expedite cell line selection to enhance your preclinical studies.
Selecting appropriate cell lines for preclinical experiments is critical but is often a hit-or-miss process. Until recently, you couldn't reliably access the genomic profiles of specific cell lines before purchasing them. This led to uncertainties regarding gene expression, mutations and other essential characteristics needed for successful experiments. Cell lines can also undergo changes and mutations over time, further complicating the selection process. This 'identity crisis' of cell lines means you need to identify and characterize their genomic profiles before you invest time and resources using them in your experiments.
Authenticated cell line 'omics data provide traceable sequencing data linked to specific cell line lots. Our collaboration with ATCC enables you to access transcriptomic datasets from human and mouse cell lines, primary cells and primary tissues.
The genomic profiles of ATCC cell lines are traceable, so you can map them back to specific lots in the biorepository freezer. This information empowers you to make informed decisions when purchasing cell lines and eliminates the need for extensive sequencing and analysis work.
Authenticated 'omics data ensures reproducibility and predictability in studies. This means you can expect consistent and reliable results because the selected cell lines carry the desired genes and traits. Our collaboration with ATCC addresses concerns about the robustness and reliability of preclinical research, as evidenced by a high prevalence of irreproducible studies. By using authenticated data, you can mitigate risks, save time and more efficiently allocate resources.
So, how can you access authenticated cell line 'omics data? It's easy—you subscribe to the ATCC Cell Line Land database. Our partnership with ATCC allows seamless access to the data and identification of the exact cell lines you need for your experiments. The database is continually expanding with thousands of new samples each year, ensuring a wide range of cell line options. You can also request specific cell lines for priority addition to the database.
When choosing cell lines, it's essential to avoid common pitfalls. Relying solely on published journal articles or assuming that public data are vetted can lead to unreliable results. You've got to trust the source material and authenticate expressions, mutations, and other traits to establish a strong foundation for your work. While using ATCC Cell Line Land may involve a slight deviation from how you usually work, its advantages far outweigh any adjustments you need to make.
Cell line selection is a critical factor for successful preclinical studies. Thanks to our collaboration with ATCC, preclinical researchers like you can now access authenticated cell line 'omics data, ensuring informed decisions before purchasing cell lines. By leveraging ATCC Cell Line Land, you'll streamline your workflows, save time and resources, and enhance the predictability and reproducibility of your studies.
Our partnership is a significant milestone on the road to advancing preclinical research and supporting your success in drug development.
If you’re a biologist studying gene function to identify new biomarkers or targets, or testing drug metabolism and toxicity, cell lines are your wingman. They provide the foundation for your experiments, helping you predict clinical response or develop new in vitro models of disease subtypes or patient segments. Yet fundamental to the value of a cell line is understanding its origin, genome and gene expression pattern to help you identify optimal cell lines for your preclinical studies.
Unfortunately, cell line misidentification, genomic aberrations and microbial contamination can compromise the value of cell lines for your experiments (1, 2). A further complication is that current ‘omics data repositories do not contain data on many cell lines. If you’re not studying cancer, you might find yourself lost since most data repositories are missing non-oncology cell line data. You’ll often come up empty-handed when searching for datasets on mouse cell lines, too. This means you need research funds not only to acquire cell lines for your experiments but also to sequence and characterize the genes in those cell lines before you can even begin experiments. This ends up consuming a lot of time and resources, slowing down your drug development research.
Build efficiency into your preclinical pipeline with high-quality cell line ‘omics data
If you depend on cell lines to support your drug development pipeline, we’ve got news that will transform your research.
We’re now offering a new tool that will streamline how you obtain and use cell line ‘omics data to plan and design your preclinical experiments. We partnered with ATCC to establish a database of transcriptomic (RNA-seq) and genomic (whole exome sequencing) datasets from the most highly utilized human and mouse cell lines and primary tissues and cells in ATCC’s collection. These include the most common cell lines, as well as novel cell lines that do not have publicly available transcriptomic data, offering unique data you can’t get your hands on elsewhere. This database is ATCC Cell Line Land.
Cell line ‘omics data from a credible source to ensure reliable research results
ATCC offers credible, authenticated and characterized cell lines, primary tissue and primary cells to enable reproducible research results. The advantage of working with ‘omics data from ATCC cell lines is that the data is derived from cell lines cultured in ISO-compliant conditions. This means the data is reliable and comes from pure, uncontaminated samples. The transcriptome or whole genome is then sequenced from the cell line or tissue, and the resulting ‘omics data is processed and curated using our stringent and rigorous methods for ‘omics data curation, structuring and integration.
“Every dataset we produce can be traced to a physical lot of cells in our bio repository. Since there are no questions about reproducibility and traceability of those materials, you end up with maximum data provenance.”
– Jonathan Jacobs, PhD, Senior Director of Bioinformatics, ATCC
Manually curated, integrated cell line ‘omics data
The ATCC Cell Line Land datasets are processed following the same high-quality data standards we apply to all QIAGEN OmicSoft Lands collections of ‘omics data, which integrate datasets from the largest public ‘omics data repositories using controlled vocabularies and extensive manual curation. Metadata for ATCC Cell Line Land datasets include standard culture conditions, extraction protocols, sample preparation and NGS library preparation. This consistency in curation increases confidence and enables flexible integration for bioinformatics projects, including AI/ML applications. You can use the data to answer your key research questions, explore genes of interest and investigate mutations that may be important to your in vitro experiments (Figure 1).
Figure 1. Box plot showing MYC gene expression across different cell lines in the human cell line collection of ATCC Cell Line Land. This example shows how you can use ATCC Cell Line Land to quickly find cell lines with either high or low expression for a gene of interest.
Tell us, we’re listening: What ATCC cell line data is most valuable to you?
The data in ATCC Cell Line Land is continually growing, with quarterly releases to include ‘omics data on 1000 new samples each year. What’s more, the data grows based on what you, as a researcher, need most. Our team takes your requests to prioritize the cell lines you want added to our ATCC Cell Line Land collection, as well as the type of experimental data you want curated and included in the database. This may include compound treatments with IC50 values or stimulations with cytokine measurements or other parameters. Contact us with your ideas.
Get in touch
Luckily, you no longer need to waste time and money dealing with public portals or taking on the sequencing of cell lines yourself. Speed up cell line characterization and efficiently plan your in vitro testing experiments with high-quality, manually curated cell line ‘omics data from ATCC Cell Line Land. Learn more about how ATCC Cell Line Land and our other integrated ‘omics data collections help you quickly glean insights from public ‘omics data. Your focus is cancer research? Explore how ATCC Cell Line Land is an excellent complement to the Cancer Cell Line Encyclopedia (CCLE) data in QIAGEN OmicSoft OncoLand.
Learn more and request a consultation to explore how ATCC Cell Line Land will streamline your in vitro experiments and accelerate your drug discovery. Read this press release to find out more about our partnership with ATCC.
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