From Variability to Verifiability: Benchmarking Gene Expression in ATCC’s Human and Mouse Cell Lines
Advances in Genome Biology and Technology (AGBT) 2026 General Meeting
Orlando, Florida, United States
February 25, 2026Abstract
Reproducibility remains a significant challenge in biomedical research, especially when working with in vitro models such as immortalized cell lines. Variations in laboratory protocols, culture conditions, passage number, and experimental workflows can lead to substantial changes in gene expression, often resulting in inconsistent or contradictory findings. This variability undermines the reliability of data and impedes progress in both fundamental research and translational efforts.
To help address this issue, we established a comprehensive reference transcriptome for human and mouse cell lines originally sourced and maintained by ATCC. Through high-quality RNA sequencing and standardized bioinformatics workflows implemented within QIAGEN OmicSoft’s ATCC Cell Line Land and ATCC Genome Portal, we produced reproducible, well-annotated gene expression profiles across a wide array of cell lines representing diverse tissues, disease contexts, and research applications.
This dataset provides a robust benchmark for evaluating gene expressions commonly used in vitro models. It supports validation of experimental results, verification of cell line identity, detection of anomalies due to contamination or misidentification, and identification of cell line–specific biomarkers to inform model selection and experimental design.
By offering a consistent reference framework, the transcriptome enhances cross-study comparability, enables integration of datasets from multiple sources, and reinforces data quality. This resource promotes reproducibility and accelerates the translation of cell-based research into meaningful biomedical advances.
Our goal in delivering this reliable and accessible transcriptomic resource is to support the scientific community in moving from variability toward verifiability, advancing reproducible research, strengthening collaboration across sectors, and ultimately contributing to improved patient outcomes.
Download the poster to learn about a reliable and accessible resources for cell line omics data.
DownloadPresenter
Ajeet Singh, PhD
Senior Scientist, ATCC
Dr. Ajeet Singh is Senior Scientist at ATCC where he is focused on providing reference-grade whole transcriptome data that is authenticated, standard, and traceable to physical source materials available in ATCC’s biorepository. Prior to joining ATCC, Dr. Singh received his PhD in Agricultural Plant Pathology where he performed research focused on epidemiology and integrated management of plants pests and diseases. He then performed postdoctoral research at the National Institute of Environmental Health Sciences and subsequently worked as a Senior Staff Scientist at the National Cancer Institute. Dr. Singh has extensive experience in biomedical research with his research career expanding an array of interrelated disciplines exploring epigenetics, chromatin and gene expression in reproductive developmental toxicology, stem cell biology, and cancer.
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