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| http://dx.doi.org/10.1093/hmg/ddy138 | DOI Listing |
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Evaluation of Reference Gene Stability for Investigations of Intracellular Signalling in Human Cancer and Non-Malignant Mesenchymal Stromal Cells.
Front Biosci (Schol Ed)
December 2024
Laboratory of Intracellular Membranes Dynamics, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia.
Background: Real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful tool for analysing target gene expression in biological samples. To achieve reliable results by RT-qPCR, the most stable reference genes must be selected for proper data normalisation, particularly when comparing cells of different types. We aimed to choose the least variable candidate reference genes among eight housekeeping genes tested within a set of human cancer cell lines (HeLa, MCF-7, SK-UT-1B, A549, A431, SK-BR-3), as well as four lines of normal, non-malignant mesenchymal stromal cells (MSCs) of different origins.
View Article and Find Full Text PDFInPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data.
Front Biosci (Schol Ed)
December 2024
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
Background: Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional gene regulation mechanism that regulates gene expression in eukaryotes by increasing the diversity and complexity of both the transcriptome and proteome. Despite the development of more than a dozen experimental methods over the last decade to identify and quantify APA events, widespread adoption of these methods has been limited by technical, financial, and time constraints. Consequently, APA remains poorly understood in most eukaryotes.
View Article and Find Full Text PDFShared Gene Expression Dysregulation Across Subtypes of Sanfilippo and Morquio Diseases: The Role of PFN1 in Regulating Glycosaminoglycan Levels.
Front Biosci (Landmark Ed)
December 2024
Department of Molecular Biology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland.
Background: Mucopolysaccharidosis (MPS) is a class of hereditary metabolic diseases that demonstrate itself by accumulating incompletely degraded glycosaminoglycans (GAGs). MPS are classified according to the kind(s) of stored GAG(s) and specific genetic/enzymatic defects. Despite the accumulation of the same type of GAG, two MPS diseases, Sanfilippo (MPS III) and Morquio (MPS IV), are further distinguished into subclasses based on different enzymes that are deficient.
View Article and Find Full Text PDFGene Fusion Detection in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines.
Front Biosci (Landmark Ed)
December 2024
Graduate School of Information Science and Technology, Osaka University, 565-0871 Suita, Osaka, Japan.
Background: Fusion genes are important biomarkers in cancer research because their expression can produce abnormal proteins with oncogenic properties. Long-read RNA sequencing (long-read RNA-seq), which can sequence full-length mRNA transcripts, facilitates the detection of such fusion genes. Several tools have been proposed for detecting fusion genes in long-read RNA-seq datasets derived from cancer cells.
View Article and Find Full Text PDFDifferential Response to Cisplatin between Co-cultured Cells and Pure Cultured Cells Based on Single-cell RNA Sequencing of Three-dimensional-cultured Breast Cancer Cells.
Front Biosci (Landmark Ed)
November 2024
Department of Breast Surgery, The First People's Hospital of Foshan, 528100 Foshan, Guangdong, China.
Objective: The current study aimed to develop an experimental approach for the direct co-culture of three-dimensional breast cancer cells using single-cell RNA sequencing (scRNA-seq).
Methods: The following four cell culture groups were established in the Matrigel matrix: the untreated Michigan Cancer Foundation (MCF)-7 cell culture group, the MCF-7 cell culture plus cisplatin group, the untreated co-culture group, and the cell co-culture plus cisplatin group. For cell co-culture, MCF-7 cells, human mammary fibroblasts, and human umbilical vein endothelial cells were mixed at a ratio of 1:1:1.
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