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LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue.
Bhamidimarri, Poorna Manasa; Salameh, Laila; Mahdami, Amena; Abdullah, Hanan Wael; Mahboub, Bassam; Hamoudi, Rifat.
Afiliação
  • Bhamidimarri PM; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
  • Salameh L; Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates.
  • Mahdami A; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
  • Abdullah HW; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
  • Mahboub B; Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates.
  • Hamoudi R; Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.
Heliyon ; 10(12): e32896, 2024 Jun 30.
Article em En | MEDLINE | ID: mdl-38988576
ABSTRACT
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Heliyon Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Emirados Árabes Unidos País de publicação: Reino Unido

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Heliyon Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Emirados Árabes Unidos País de publicação: Reino Unido