Validating Multiple Myeloma Cell Lines

Data generated from RNA-Seq was used to validate the MM.1S, OPM-2, and RPMI-8226 cells. Base-calling and variant determination was performed using Illumina’s RTA version 1.17.21.3, and the MAPRSeq bioinformatics pipeline (http://bioinformaticstools.mayo.edu/research/maprseq) as described (23 (link)). Variants were compared to RNA-Seq variants present in the Cancer Cell Line Encyclopedia (portals.broadinstitute.org/ccle; (25 )) utilizing publicly available tools from Galaxy (use.galaxy.org). Known translocations were confirmed using gene fusion predictions resulting from the MAPRSeq pipeline, and also compared against CCLE gene fusion predictions. 3T3-L1 cells were from ATCC (www.atcc.org). 5TGM1 cells have not been validated at this time.

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Fairfield H., Dudakovic A., Khatib C.M., Farrell M., Costa S., Falank C., Hinge M., Murphy C.S., DeMambro V., Pettitt J.A., Lary C.W., Driscoll H.E., McDonald M.M., Kassem M., Rosen C., Andersen T.L., van Wijnen A.J., Jafari A, & Reagan M.R. (2020). Myeloma-modified adipocytes exhibit metabolic dysfunction and a senescence-associated secretory phenotype (SASP). Cancer research, 81(3), 634-647.

Publication 2020

RTA version 1.17.21.3

3t3 l1 cells Cancer Cell line Cells Gene fusion Rna seq Translocations

Corresponding Organization :

Other organizations : Maine Medical Center Research Institute, Tufts University, University of Maine, Mayo Clinic, Novo Nordisk Foundation, University of Copenhagen, Vejle Sygehus, Garvan Institute of Medical Research, Norwich University Applied Research Institute, University of Southern Denmark, Odense University Hospital, Lillebaelt Hospital

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Variable analysis

independent variables

RNA-Seq data used to validate the MM.1S, OPM-2, and RPMI-8226 cells

dependent variables

Variants compared to RNA-Seq variants present in the Cancer Cell Line Encyclopedia
Known translocations confirmed using gene fusion predictions from the MAPRSeq pipeline and compared against CCLE gene fusion predictions

control variables

3T3-L1 cells from ATCC
5TGM1 cells have not been validated at this time

positive controls

None specified

negative controls

None specified

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