PreprintBrief ReportVersion 1This version is not peer-reviewed
Resource: Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease
Version 1
: Received: 4 September 2024 / Approved: 5 September 2024 / Online: 6 September 2024 (05:46:42 CEST)
How to cite:
Scott, A. F.; Mohr, D. W.; Littrell, W. A.; Babu, R.; Kokosinski, M.; Stinnett, V. L.; Madhiwala, J.; Anderson, J.; Zou, Y. S.; Gabrielson, K. Resource: Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease. Preprints2024, 2024090416. https://doi.org/10.20944/preprints202409.0416.v1
Scott, A. F.; Mohr, D. W.; Littrell, W. A.; Babu, R.; Kokosinski, M.; Stinnett, V. L.; Madhiwala, J.; Anderson, J.; Zou, Y. S.; Gabrielson, K. Resource: Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease. Preprints 2024, 2024090416. https://doi.org/10.20944/preprints202409.0416.v1
Scott, A. F.; Mohr, D. W.; Littrell, W. A.; Babu, R.; Kokosinski, M.; Stinnett, V. L.; Madhiwala, J.; Anderson, J.; Zou, Y. S.; Gabrielson, K. Resource: Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease. Preprints2024, 2024090416. https://doi.org/10.20944/preprints202409.0416.v1
APA Style
Scott, A. F., Mohr, D. W., Littrell, W. A., Babu, R., Kokosinski, M., Stinnett, V. L., Madhiwala, J., Anderson, J., Zou, Y. S., & Gabrielson, K. (2024). Resource: Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease. Preprints. https://doi.org/10.20944/preprints202409.0416.v1
Chicago/Turabian Style
Scott, A. F., Ying S Zou and Kathy Gabrielson. 2024 "Resource: Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease" Preprints. https://doi.org/10.20944/preprints202409.0416.v1
Abstract
The rat osteosarcoma cell line UMR-106 is widely used for the study of bone cancer biology. We have characterized UMR-106 with a combination of optical genome mapping (OGM), long-read sequencing (for identification of variants and 5mC methylation), and short-read RNA sequencing for expression. Genome sequence was compared to a Sprague-Dawley control animal, the strain from which UMR-106 was derived, and expression data were compared to a public rat osteoblast dataset. Using the COSMIC database to identify the most affected genes in human osteosarcomas (OS) we found somatic mutations in Tp53 and H3f3a in UMR-106. OGM identified a relatively small number of differences between the cell line and strain-matched control animal but did detect a ~45 Mb block of amplification that included Myc on chromosome 7 which was confirmed by long-read sequencing. The amplified region included several genes reported as biomarkers in human osteosarcoma, many of which showed increased transcription. A comparison of 5mC methylation from the nanopore reads of tumor and control highlighted several genes with distinct differences including the OS marker Cdkn2a. This dataset illustrates the value of long DNA methods for the characterization of cell lines and how inter-species analysis can inform about the genetic nature underlying mutations that underpin specific tumor types. The data should be a valuable resource for investigators studying osteosarcoma, in general, and specifically the UMR-106 model.
Biology and Life Sciences, Biology and Biotechnology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
