Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analyses of anti-adipogenic effects of oleuropein in human mesenchymal stem-cells

ABSTRACT: The main goal of the present work was to use an in vitro adipogenic-differentiation mode, with mesenchymal stem-cells (MSC) from human bone-marrow, to study whole-transcriptomic differential gene-expression when such cells are induced to differentiate into adipocytes in absence or presence of oleuropein. See details below. This work is complementary to a previously published one (Casado-Daz et al, 2016): Casado-DÃaz, A., Anter, J., MÃ¼ller, S., Winter, P., Quesada-GÃ³mez, J. M. and Dorado, G. (2016): Transcriptomic analyses of adipocyte differentiation from human mesenchymal stromal-cells (MSC). Journal of Cellular Physiology 9999: 1-14. DOI: 10.1002/jcp.25472. It corresponds to EMBL-EBI ArrayExpress accession E-MTAB-4884.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Homo sapiens

SUBMITTER: Nicolas Krezdorn

PROVIDER: E-MTAB-5211 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic analyses of adipocyte differentiation from human mesenchymal stromal-cells (MSC)

Project description:Adipogenesis is a physiological process required for fat-tissue development, mainly involved in regulating the organism energetic-state. Abnormal distribution-changes and dysfunctions in such tissue are associated to different pathologies. Adipocytes are generated from progenitor cells, via a complex differentiating process not yet well understood. Therefore, we investigated differential mRNA and miRNA expression patterns of human mesenchymal stromal-cells (MSC) induced and not induced to differentiate into adipocytes by next (second)-generation sequencing. A total of 2,866 differentially-expressed genes (101 encoding miRNA) were identified, with 705 (46 encoding miRNA) being upregulated in adipogenesis. They were related to different pathways, including PPARG, lipid, carbohydrate and energy metabolism, redox, membrane-organelle biosynthesis and endocrine system. Downregulated genes were related to extracellular matrix and cell migration, proliferation and differentiation. Analyses of mRNA-miRNA interaction showed that repressed miRNA-encoding genes can act downregulating PPARG-related genes; mostly the PPARG activator (PPARGC1A). Induced miRNA-encoding genes regulate downregulated genes related to TGFB1. These results shed new light to understand adipose-tissue differentiation and physiology, increasing our knowledge about pathologies like obesity, type-2 diabetes and osteoporosis.

2016-08-31 | E-MTAB-4884 | biostudies-arrayexpress

Regulation of the cardiac transcriptome by the E3 ubiquitin ligase Huwe1.

Project description:Analysis of the cardiac transcriptome by heart-specific acute genetic ablation of Huwe1 in adult male mice employing a tamoxifen-inducible Cre-loxP system.

2016-09-30 | E-MTAB-5112 | biostudies-arrayexpress

RNA-seq of of human (Homo sapiens), gorilla (Gorilla gorilla) and cynomolgus macaque (Macaca fascicularis) iPSC and iPSC-derived NPC cell lines

Project description:RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Bulk RNA-seq libraries of iPSCs and NPCs were generated using prime-seq protocol (Janjic et al. 2022).

2023-11-23 | E-MTAB-13494 | biostudies-arrayexpress

Variations of secretome profiles according to conditioned medium preparation: the example of human mesenchymal stem cell derived adipocytes

Project description:One challenging point in analysing cellular secretome collected as conditioned medium is cross contamination by cell culture media components, especially bovine serum proteins. A common approach for serum removal is to wash the cells, an alternative is to grow cells using serum-free conditions. Given that the sample processing may influence the phenotype of cells and thus the secretome, it is important to establish the optimal protocol for each cell type. In this study, we compared two methods for preparing conditioned medium from human adipocytes derived from mesenchymal stem cells. Cells were either washed twice with PBS or cultured the last four days of differentiation in serum free adipogenic medium. Gene expression of the cells was evaluated by using real time PCR and one dimensional LC-MS/MS was used to compare secreted proteins present in the culture supernatants. Surprisingly, results showed significant differences in gene expression patterns of the cells and in protein content of the conditioned media and suggested that PBS washes induced severe modifications of the phenotype of cells and thus changes in protein secretion profiles. These data emphasize the significant variations in protein species related to cell manipulations and underline the importance of procedure optimization prior to any proteomic investigation.

2015-07-03 | PXD002217 | Pride

Influenza infection rewires energy metabolism and induces browning features in adipose cells and tissues

Project description:Influenza A viruses cause epidemics and pandemics with damaging health and economic impacts. Alike any obligate intracellular pathogen, IAVs hijack host cell machinery and energetic resources to multiply within, and eventually exit, the host. Increased fatty acid and cholesterol synthesis, as well as increased glucose metabolism have been identified as the major metabolic changes induced by infection. Besides these effects on metabolism, IAV infection also triggers a variety of innate defense mechanisms within the host cell. Although mainly defined as a virus of the respiratory tract, with airway epithelial cells being its prime cellular habitat, complications outside the site of infection have also been reported. However, whether influenza on its own may impact on endocrine tissues and, thereby, lead to metabolic complications, has never been investigated. Here, we compared the response of preadipocytes and adipocytes to IAV infection, in terms of transcriptomic profiles and bioenergetics. The results showed that IAV triggers a browning adipogenesis process, leading to metabolic reprogramming of the adipose tissue resulting in long-lasting alterations of body metabolism. We conclude that the adipose tissue might be an undervalued organ in influenza pathophysiology.

2019-07-20 | E-MTAB-6646 | biostudies-arrayexpress

Time-course transcriptome analysis of a human neuronal cell line with RFX2 KO

Project description:RNA-seq analysis on a human neuronal cell line derived from fetal mesencephalon (LUHMES) wild type and RFX2 knockout from day 0 to day 6.

2024-01-31 | E-MTAB-11546 | biostudies-arrayexpress

Sequencing data for single cells and DNA-functionalized microbeads encapsulated in hydrogel droplets.

Project description:DNA barcodes can be used to identify single cells in a sequencing data space while optical codes can be used to track single live cells in an image data space. We have developed dual image and DNA (ID)-coding, which identifies individual single cells in both live image and sequencing data spaces. Samples provided here are relevant to proof-of-concept studies of ID-coding presented in the associated publication. DNA barcoded micro-particles were encapsulated in hydrogel droplets with or without single cells. The hydrogel droplets were then subjected to “single-droplet sequencing” where whole polyA-bearing nucleic acid components within a hydrogel droplet (i.e. mRNA from cells and synthetic DNA on beads) were concatenated by the same cell barcodes.

2023-12-11 | E-MTAB-12988 | biostudies-arrayexpress

Human iPSC-derived cardiomyocytes of peripartum cardiomyopathy patients reveal aberrant expression of sterol and lipid metabolism pathways

Project description:To identify the consequences of mechanical stress of differentiated cardiac muscles from healthy- and PPCM individuals. RNA-sequencing data was obtained from 4 individuals from 2 families. Each family had one member with PPCM and one healthy. Individual 1 and 2 were sisters, one healthy, one with PPCM. Individual 3 and 4 were a healthy mother and PPCM daughter. From each patient 4, 6, 1 and 3 clones were derived, respectively. From each clone multiple pairs of cells were collected and either stretched or left static to a total of 40 pairs, with 2 unpaired static samples.

2020-12-08 | E-MTAB-9053 | biostudies-arrayexpress

Cationic amino acid transporter-1 influences the leptin transport in an iPSC-derived in vitro blood-brain barrier model

Project description:Total RNAs extracted from iPSC-derived BMEC-like cells with or without 17β-estradiol treatment were collected and analyzed using RNA sequencing.

2022-05-16 | E-MTAB-11691 | biostudies-arrayexpress

Gene expression analysis during adipocytic differentiation of human bone marrow cells (hMSC-TERT)

Project description:We have employed whole genome microarray to identify changes in gene expression in human bone marrow MSCs (hMSC-TERT) during adipocytic differentiation in culture for 7 days Human MSC line (hMSC-TERT) were subjectd to adipocytic differentiation for 7 days, subsequently, RNA was extracted using Norgen total RNA isolation kit. Extracted RNA was labeled and then hybridized to the one-color Agilent Human GE 8x60K Microarray chip.

2014-09-09 | E-GEOD-59450 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data