Normalization of mRNA profiling data remains an open issue, which turns critical when comparing divergent samples or mRNA populations with different complexities. To address this question, we generated samples with different RNA amounts and complexities by subcellular fractionation of cytoplasmic RNA into the mutually exclusive ribosome-free and polysome-bound RNA pools. For each of the 563 mRNAs analyzed, the hybridization signal corresponding to the cytoplasmic sample equals the sum of signals from the ribosome-free plus the polysome-bound targets (cytoplasmic mRNA = ribosome-free mRNA + polysome-bound mRNA). This intuitive equation was fulfilled only after data normalization following "spiking" of the samples with an exogenous RNA. This is the first demonstration that spiking allows one to correct not only for differences in reaction efficiencies but also to reflect the variations in amount and complexity between the initial mRNA populations.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.2144/01306rr03 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
High glucose/ChREBP-induced Hif-1α transcriptional activation in CD4 T cells reduces the risk of diabetic kidney disease by inhibiting the Th1 response.
Diabetologia
January 2025
Kidney Transplantation Center, Department of Urology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
Aims/hypothesis: Diabetic kidney disease (DKD) features intrarenal inflammation, in which T cells play a part. Hypoxia-inducible factor-1α (HIF-1α), a key transcription factor regulating cellular responses to hypoxia, is reportedly involved in the course of inflammation. The role of HIF-1α in DKD has been investigated, but the conclusions are controversial so far.
View Article and Find Full Text PDFIntegrated analysis of proteome and transcriptome profiling reveals pan-cancer-associated pathways and molecular biomarkers.
Mol Cell Proteomics
January 2025
State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China. Electronic address:
Understanding dysregulated genes and pathways in cancer is critical for precision oncology. Integrating mass spectrometry-based proteomic data with transcriptomic data presents unique opportunities for systematic analyses of dysregulated genes and pathways in pan-cancer. Here, we compiled a comprehensive set of datasets, encompassing proteomic data from 2,404 samples and transcriptomic data from 7,752 samples across 13 cancer types.
View Article and Find Full Text PDFComprehensive transcriptome analysis reveals lncRNA-mRNA interactions and immune response mechanisms in Mytilus coruscus upon Vibrio alginolyticus infection.
Dev Comp Immunol
January 2025
National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China. Electronic address:
Long non-coding RNAs (lncRNAs) play diverse biological roles within cells. Despite not encoding proteins, they are crucial in regulating gene expression, chromatin structure and function, cell differentiation and development, and the occurrence of diseases. Vibrio alginolyticus (V.
View Article and Find Full Text PDFCurrent and Future Role of Circulating DNA in the Diagnosis and Management of Urothelial Carcinoma.
Am Soc Clin Oncol Educ Book
January 2025
Division of Oncology, Department of Medicine, University of Washington, Seattle, WA.
The growing sophistication of tumor molecular profiling has helped to slowly transition oncologic care toward a more personalized approach in different tumor types, including in bladder cancer. The National Comprehensive Cancer Network recommends that all patients with stage IVA and stage IVB urothelial carcinoma have molecular analysis that integrates at least testing to help facilitate the selection of future therapeutic options. Sequencing of tumor-derived tissue is the mainstay to obtain this genomic testing, but as in other cancers, there has been extensive research into the integration of liquid biopsies in longitudinal management.
View Article and Find Full Text PDFComprehensive analysis of ceRNA Networks in UCEC: Prognostic and therapeutic implications.
PLoS One
January 2025
Department of Reproductive Medicine, Guangzhou Women and Children's Medical center Liuzhou Hospital, Liuzhou, Guangxi, China.
Endometrial cancer (UCEC) is the most prevalent gynecological malignancy in high-income countries, and its incidence is rising globally. Although early-stage UCEC can be treated with surgery, advanced cases have a poor prognosis, highlighting the need for effective molecular biomarkers to improve diagnosis and prognosis. In this study, we analyzed mRNA and miRNA sequencing data from UCEC tissues and adjacent non-cancerous tissues from the TCGA database.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!