Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis

Marcon, Bruna Hilzendeger; Spangenberg, Lucía; Bonilauri, Bernardo; Robert, Anny Waloski; Angulski, Addeli Bez Batti; Cabo, Guillermo Cabrera; Cofré, Axel R.; Bettes, Paulo Sergio Loiacono; Dallagiovanna, Bruno; Shigunov, Patrícia

doi:10.1016/j.dib.2019.105053

Cited by 8 publications

(17 citation statements)

References 7 publications

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“…Transcriptomic analysis confirmed the upregulation of key transcriptional factors during early adipogenesis. Different analysis demonstrated that KLF15 expression was detected in the first 24 h of induction ( Ambele et al, 2016 ; Marcon et al, 2019 , 2020 ), and remained upregulated after 3 ( Spangenberg et al, 2013 ), 7, 14 and 21 ( Ambele et al, 2016 ) days of adipogenic treatment. An augmentation of LMO3, FOXO1, ZBTB16 ( Ambele et al, 2016 ; Marcon et al, 2019 ) CEBPB and CEBPD ( Marcon et al, 2019 ) mRNA was also detected in the total and in the polysome-associated mRNA fraction ( Marcon et al, 2019 ), suggesting not only an upregulation in terms of mRNA abundance but also in protein synthesis rate.…”

Section: Gene Expression Profile In Adipogenesis Of Mscmentioning

confidence: 99%

“…The mRNAs associated with polysomes and the rate of translation of the transcripts may also be regulated, modulating protein synthesis. The use of methodologies as the polysome profiling ( Spangenberg et al, 2013 ; Marcon et al, 2020 ) and the ribosome profiling ( Ingolia et al, 2009 , 2012 ; Ingolia, 2016 ; Marcon et al, 2017 ) are interesting to investigate these aspects of gene expression. The analysis and comparison of total or ribosome free mRNA fraction with the one associated to polysomes or ribosomes may provide important information about the level at which genes are being regulated, identifying mechanisms of translational efficiency ( Marcon et al, 2017 ) and of coordinated/opposite actions of the transcriptional and the post-transcriptional mechanisms ( Marcon et al, 2017 ; Pereira et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Adipogenesis, Osteogenesis, and Chondrogenesis of Human Mesenchymal Stem/Stromal Cells: A Comparative Transcriptome Approach

Robert

Marcon

Dallagiovanna

et al. 2020

Front. Cell Dev. Biol.

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Adipogenesis, osteogenesis and chondrogenesis of human mesenchymal stem/stromal cells (MSC) are complex and highly regulated processes. Over the years, several studies have focused on understanding the mechanisms involved in the MSC commitment to the osteogenic, adipogenic and/or chondrogenic phenotypes. High-throughput methodologies have been used to investigate the gene expression profile during differentiation. Association of data analysis of mRNAs, microRNAs, circular RNAs and long non-coding RNAs, obtained at different time points over these processes, are important to depict the complexity of differentiation. This review will discuss the results that were highlighted in transcriptome analyses of MSC undergoing adipogenic, osteogenic and chondrogenic differentiation. The focus is to shed light on key molecules, main signaling pathways and biological processes related to different time points of adipogenesis, osteogenesis and chondrogenesis.

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Section: Gene Expression Profile In Adipogenesis Of Mscmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Adipogenesis, Osteogenesis, and Chondrogenesis of Human Mesenchymal Stem/Stromal Cells: A Comparative Transcriptome Approach

Robert

Marcon

Dallagiovanna

et al. 2020

Front. Cell Dev. Biol.

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“…NEFM, GRIN2A, NPTX1, NRG1, and NGF genes are related to nerve cell development and nerve signal transmission. NEFM is associated with neural maturation ( Urrutia et al, 2019 ; Kawase-Koga et al, 2020 ) and is down-regulated after early adipogenic differentiation ( Urrutia et al, 2019 ; Marcon et al, 2020 ; Sadeghi et al, 2020 ; Nie et al, 2021 ). GRIN2A is found in nerve cells (neurons) in the brain and spinal cord and one component of a subset of NMDA receptors.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics Analysis Identified miR-584-5p and Key miRNA-mRNA Networks Involved in the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells

et al. 2021

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Human periodontal ligament cells (PDLCs) play an important role in periodontal tissue stabilization and function. In the process of osteogenic differentiation of PDLSCs, the regulation of molecular signal pathways are complicated. In this study, the sequencing results of three datasets on GEO were used to comprehensively analyze the miRNA-mRNA network during the osteogenic differentiation of PDLSCs. Using the GSE99958 and GSE159507, a total of 114 common differentially expressed genes (DEGs) were identified, including 62 up-regulated genes and 52 down-regulated genes. GO enrichment analysis was performed. The up-regulated 10 hub genes and down-regulated 10 hub genes were screened out by protein-protein interaction network (PPI) analysis and STRING in Cytoscape. Similarly, differentially expressed miRNAs (DEMs) were selected by limma package from GSE159508. Then, using the miRwalk website, we further selected 11 miRNAs from 16 DEMs that may have a negative regulatory relationship with hub genes. In vitro RT-PCR verification revealed that nine DEMs and 18 hub genes showed the same trend as the RNA-seq results during the osteogenic differentiation of PDLSCs. Finally, using miR-584-5p inhibitor and mimics, it was found that miR-584-5p negatively regulates the osteogenic differentiation of PDLSCs in vitro. In summary, the present results found several potential osteogenic-related genes and identified candidate miRNA-mRNA networks for the further study of osteogenic differentiation of PDLSCs.

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“…hASCs were isolated from adipose tissue obtained from female donors who underwent liposuction surgery, as previously described[ 13 ]. Informed consent was provided by each donor.…”

Section: Methodsmentioning

confidence: 99%

“…Immunophenotypic characterization was based on the parameters established for defining mesenchymal stem cells, as indicated by the International Society for Cellular Therapy[ 14 ]. The protocol used followed that previously established in our laboratory[ 13 ]. CD90, CD105, CD73 and CD140b were considered positive markers, while the negative markers were CD19, CD11b, HLA-DR, CD45, CD34 and CD31.…”

Section: Methodsmentioning

confidence: 99%

Influence of donor age on the differentiation and division capacity of human adipose-derived stem cells

Horinouchi¹,

Barisón²,

Robert³

et al. 2020

WJSC

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Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis

Cited by 8 publications

References 7 publications

Adipogenesis, Osteogenesis, and Chondrogenesis of Human Mesenchymal Stem/Stromal Cells: A Comparative Transcriptome Approach

Adipogenesis, Osteogenesis, and Chondrogenesis of Human Mesenchymal Stem/Stromal Cells: A Comparative Transcriptome Approach

Bioinformatics Analysis Identified miR-584-5p and Key miRNA-mRNA Networks Involved in the Osteogenic Differentiation of Human Periodontal Ligament Stem Cells

Influence of donor age on the differentiation and division capacity of human adipose-derived stem cells

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