Bulk RNAseq was performed on frozen muscle biopsy specimens as previously described.6 (link),9 (link)–13 (link) Briefly, RNA was extracted with TRIzol. Libraries were either prepared with the NeoPrep system according to the TruSeq Stranded mRNA Library Prep protocol (Illumina, San Diego, CA) or with the NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7490, and #E7760).
Pinal-Fernandez I., Muñoz-Braceras S., Casal-Dominguez M., Pak K., Torres-Ruiz J., Musai J., Dell’Orso S., Naz F., Islam S., Gutierrez-Cruz G., Cano M.D., Matas-Garcia A., Padrosa J., Tobías-Baraja E., Garrabou G., Aldecoa I., Espinosa G., Simeon-Aznar C.P., Guillen-Del-Castillo A., Gil-Vila A., Trallero-Araguas E., Christopher-Stine L., Lloyd T.E., Liewluck T., Naddaf E., Stenzel W., Greenberg S.A., Grau J.M., Selva-O’Callaghan A., Milisenda J.C, & Mammen A.L. (2024). Pathogenic autoantibody internalization in myositis. medRxiv.
Other organizations :
Johns Hopkins Medicine, Johns Hopkins University, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Services Hospital, Centre for Biomedical Network Research on Rare Diseases, Consorci Institut D'Investigacions Biomediques August Pi I Sunyer, Universitat de Barcelona, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Mayo Clinic in Arizona, Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Brigham and Women's Hospital, Harvard University, Boston Children's Hospital
Library preparation method (NeoPrep system vs. NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit)
dependent variables
Transcriptomic profiles of muscle biopsy specimens
control variables
Frozen muscle biopsy specimens
Previously described protocol for bulk RNAseq
controls
No positive or negative controls were explicitly mentioned in the provided information.
Annotations
Based on most similar protocols
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