The NCI’s Division of Cancer Biology (DCB), Physical Sciences-Oncology Network (PS-ON) program has established a PS-ON Bioresource Core Facility (PBCF) that provides a panel of 49 model cell lines to affiliated investigators. The PBCF cell lines have been used by investigators within PS-ON network to perform a variety of physical science based studies. To further increase the value of the PBCF cell lines, the NCI has complemented these efforts to characterize the genetics, physical properties, and proteomics of subsets of these cell lines. The data from the genomic and physical characterization studies have been made publicly available through the PS-ON Data Coordinating Center (PS-ON DCC) at https://nciphub.org/groups/nci_physci/psondcc. In addition, the genomic data has been made available thought the NCBI Short Read Archive (SRA), consistent with the NIH Genome Data Sharing Policy.
The physical characterization project measured differences in physical (morphological and mechanical) properties of cells grown on substrates of varying stiffness, i.e., hydrogels with different viscoelastic properties and integrin ligands (collagen or fibronectin). Assays were conducted on 30 cell lines from the PBCF panel, grown on seven different substrates.
The goal of PBCF cell line proteomics characterization project, is to extend the studies done in the physical characterization project to include proteomic and phosphoproteomic analysis of nine cell lines grown under the same seven conditions that were used for the physical characterization experiment. Also included in this proteomics characterization project was a requirement to harvest and freeze cell pellets of cells from nine cell lines, grown on each of the seven growth conditions, to be used for subsequent RNA sequencing work. 63 cell pellets have been collected and stored at -80 in the lab of the proteomics subcontractor (Stanford University, subcontract 15X009). Additionally, the proteomics subcontractor experimentally confirmed that the protocol chosen to harvest and freeze the pellets yields RNA of sufficient purity for downstream analysis. These pellets will be the source of the RNA to be characterized as part of this RNA sequencing project.
mRNA Sequencing (mRNA-Seq) and miRNA Sequencing (miRNA-Seq) characterization of the RNA samples are expected to complement and extend the data sets obtained from both the physical characterization project and the proteomic characterization project. This characterization will further increase the value not only of the PBCF cell line but also the experiments that have already been and are being conducted on the PBCF cell lines by the research community.