Unfolding the Whole Transcriptome of the American Type Culture Collection Cell Line Land for its Application as a Molecular Reference Standard in Next-generation Biomedicine Research

In the cell biology research space, the use of unauthenticated biological reference materials, irregularities in crucial related metadata, and frequent gaps in data provenance often raise questions as to the credibility and reproducibility of experimental data. To address this problem, we have begun efforts to characterize the whole transcriptomes of all cell lines and primary cells held within ATCC’s (American Type Culture Collection) cell biology collection to develop an authenticated application data resource to be used as a molecular reference standard. Here, we present our initial analysis of authenticated whole transcriptome (RNA-seq) datasets produced from 62 human kidney cell lines, including primary cells, found in ATCC’s biorepository. These diverse datasets, represented by ATCC Cell Line Land, include the first comprehensive collection of reference transcriptomes for use by kidney biology researchers and are available through QIAGEN’s OmicSoft platform. Multiple biological replicates for each cell line are included to help establish a baseline for a wide range of cell lines under typical cell culture conditions. ATCC Cell Line Land includes transcript and gene expression count data, RNA-seq variant calls, raw sequencing data, and detailed metadata on laboratory methods employed such as the total cell counts, RNA extraction methods, RIN scores, number of replicates, tissue/cell-type information, disease association, passage number, catalog number, lot number, growth media, culture conditions, and cryopreservation conditions. Furthermore, all biological replicate data included in this resource are produced using a common, standardized RNA extraction, library prep, sequencing, and bioinformatics workflow, thereby enabling comparative transcriptomics of these data at scale. ATCC Cell Line Land is a first-of-its-kind joint venture between ATCC and QIAGEN Digital Insights aimed at providing reference-grade whole transcriptome data that is authenticated, standardized, and traceable to physical source materials available in ATCC’s biorepository.