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. 2019 Dec 31;28:105053. doi: 10.1016/j.dib.2019.105053

Specifications Table

Subject Biology
Specific subject area Molecular Biology, Cell Biology, Adult Stem Cells, Transcriptome, Translatome
Type of data Table
Chart
Graph
Figure
How data were acquired Sucrose density gradient elaboration (BioComp Model 108 Gradient Master ver. 5.3)
Ultracentrifugation (HIMAC CP80WX, HITACHI)
Fractionation of sucrose gradient (ISCO Model 160 Gradient Former Foxy Jr. Fraction Collector)
RNA quality control (Agilent 2100 Bioanalyzer, Agilent)
RNA-Seq (Illumina HiSeq 2500 System)
Data analysis (Rsubread package; Bioconductor R package edgeR)
RT-qPCR (SYBR® Green PCR Master Mix, Applied Biosystems®; LightCycler® 96, Roche)
Data format Raw
Analyzed
Parameters for data collection Human adipose -derived stem cells (hASCs) were isolated from adipose tissue obtained from three healthy female donors that underwent liposuction surgery. Then hASCs were treated with maintenance (control – CT), adipogenic (ADI) or osteogenic (OST) induction medium for 24 h and submitted to total, ribosome-free, monosomal and polysomal RNA isolation.
Description of data collection hASCs were kept in control medium or induced to adipogenesis or osteogenesis for 24 hours. The samples were submitted to sucrose density fractionation and the polysome profile was recorded to identify and to separate the ribosome-free, monosomal and polysomal RNA. Total RNA of each sample was also isolated. RNA-quality was checked and RNA-Seq were performed. The sequencing accuracy and the reproducibility of biological samples were also evaluated. The validation of RNA-Seq data was also performed by RT-qPCR.
Data source location Institution: Instituto Carlos Chagas - FIOCRUZ-PR
City/Town/Region: Curitiba, Paraná
Country: Brazil
Data accessibility Raw RNA-Seq data can be downloaded at the ArrayExpress repository under the ID E-MTAB-6298. Direct URL to data: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6298/[2018].
Raw RT-qPCR dataset has been deposited in the Mendeley Data Repository: “DIB – RT-qPCR dataset”, Mendeley Data, https://data.mendeley.com/datasets/57bfj2z2kr/1
Related research article A.W. Robert, A.B.B. Angulski, L. Spangenberg, P. Shigunov, I.T. Pereira, P·S.L. Bettes, H. Naya, A. Correa, B. Dallagiovanna, M.A. Stimamiglio, Gene expression analysis of human adipose tissue-derived stem cells during the initial steps of in vitro osteogenesis, Sci. Rep. 8 (2018) 4739. https://doi.org/10.1038/s41598-018-22991-6.
B.H. Marcon, P. Shigunov, L. Spangenberg, I.T. Pereira, A.M. de Aguiar, R. Amorín, C.K. Rebelatto, A. Correa, B. Dallagiovanna, Cell cycle genes are downregulated after adipogenic triggering in human adipose tissue-derived stem cells by regulation of mRNA abundance, Sci. Rep. 9 (2019) 5611. https://doi.org/10.1038/s41598-019-42005-3.