Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human ASCs expanded with 10% FBS and in FBS-deprived condition

ABSTRACT: In this experiment we determined the effects of FBS supplementation and subsequent deprivation (after second passage) on the whole transcriptome, including comprehensive mRNA and miRNA profiling.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Alina Mieczkowska

PROVIDER: E-MTAB-6436 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells.

Mieczkowska Alina A Schumacher Adriana A Filipowicz Natalia N Wardowska Anna A Zieliński Maciej M Madanecki Piotr P Nowicka Ewa E Langa Paulina P Deptuła Milena M Zieliński Jacek J Kondej Karolina K Renkielska Alicja A Buckley Patrick G PG Crossman David K DK Crowley Michael R MR Czupryn Artur A Mucha Piotr P Sachadyn Paweł P Janus Łukasz Ł Skowron Piotr P Rodziewicz-Motowidło Sylwia S Cichorek Mirosława M Pikuła Michał M Piotrowski Arkadiusz A

Scientific reports 20180727 1

Adipose-derived stem cells (ASCs) have become an important research model in regenerative medicine. However, there are controversies regarding the impact of prolonged cell culture on the ASCs phenotype and their differentiation potential. Hence, we studied 10 clinical ASCs replicates from plastic and oncological surgery patients, in six-passage FBS supplemented cultures. We quantified basic mesenchymal cell surface marker transcripts and the encoded proteins after each passage. In parallel, we i ...[more]

PMID: 30054533

Similar Datasets

miRNA-seq of human ASCs expanded with 10% FBS and in FBS-deprived condition.

Project description:In this experiment we determined the effects of FBS supplementation and subsequent deprivation (after second passage) on the whole transcriptome, including comprehensive mRNA and miRNA profiling.

2018-08-09 | E-MTAB-6390 | biostudies-arrayexpress

RNA-seq of human BR.1N and HaCaT cell lines treated with zebularine against untreated controls

Project description:The experimental design demonstrates that zebularine, a DNA methyltransferase inhibitor, promotes regeneration in the mouse and that retinoic acid and zebularine synergistically accelerate this process.

2019-11-02 | E-MTAB-6832 | biostudies-arrayexpress

Microarray gene expression profiles of adipose-derived mesenchymal stem cells from LEW and PVG rats upon 24h and 48h LPS stimulation

Project description:We have extended our investigation to differential immunogenicity between tolerogenic PVG rats and immunogenic LEW rats by analyzing gene expression in adipose-derived mesenchymal stem cells (ASCs) with LPS stimulation. Furthermore, to establish a direct link between gene expression and immunogenic functional annotation, ASCs from LEW and PVG rats were obtained, and the effects of inherent difference and LPS treatment on global gene expression were evaluated using microarray analyses. We analyzed microarray gene expression profiles of ASCs from 3 LEW and 3 PVG rats of 8-week age and separated ASCs from each individual into four conditions, 24h and 48h control, 24h and 48h with 1 μg/ml LPS stimulation. The total RNA samples of triplicate ASCs isolated from LEW and PVG with and without LPS treatment were pooled in each condition and the global gene expression profiles were analyzed using microarray.

2012-10-02 | E-GEOD-41262 | biostudies-arrayexpress

A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules

Project description:Adipose stem cells (ASCs) and adipocytes play a crucial role in maintaining energy balance. We aim to examine the temporal relationship between gene expression and histone modification transitions during in vitro differentiation of human ASCs into adipocytes. Here, we examine by RNAseq proliferating ASCs (Day -2 prior to adipogenic induction), confluent ASCs (Day 0, adipogenic induction), pre-adipocytes (Day 3) and maturing adipocytes (Day 9). We find 1060, 5452 and 2216 genes differentially expressed between D-2/D0, D0/D3 and D3/D9 respectively. We identify gene clusters with distinct and dynamic expression patterns. In particular, adipogenic induction is marked by temporal waves of gene induction and downregulation. We report two types of transcriptional waves: (i) those showing transient induction or inactivation at D0, D3 or D9, and involved in sensory perception and immune response functions; and (ii) those showing long-lived induction or repression at these time points. Our data reveal a dynamic network of gene regulation during adipogenesis, involving signaling, immune and developmental processes. We identify 15 unique epigenetic states using Hidden Markov Modeling which reflects an epigenetically highly organised genome showing enhancer states are commonly consecutive. A heatmap for the abundance of epigenetic states for the expression clusters reveals a link between expression and epigenetic marking of the state suggesting an increase in the number of number of chromatin states with increase in expression. Our data point to a model of increased epigenetic complexity associated with gene expression. Examination of expression of profiles of ASCs across differentiation

2014-12-10 | E-GEOD-60237 | biostudies-arrayexpress

Evaluation of secretomes derived from human dermal and adipose tissue mesenchymal stem/stromal cells for skin wound healing: Not as effective as cells

Project description:Although the paracrine effects of mesenchymal stem/stromal cells (MSCs) have been recognized as crucial mediators of their regenerative effects on tissue repair, the potential of MSC secretomes as effective substitutes for cellular therapies remains underexplored. In this study, we compared MSCs from the human dermis (DSCs) and adipose tissue (ASCs) with their secretomes regarding their efficacy for skin wound healing using a translationally-relevant murine model. Proteomic analysis revealed that while there was a substantial overlap in protein composition between DSC and ASC secretomes, specific proteins associated with wound healing and angiogenesis were differentially expressed. Despite a similar angiogenic potential in vivo, DSC- and ASC-secretomes were found to be less effective than cells in accelerating wound closure and promoting tissue remodeling. Overall, secretome-treated groups showed intermediary results between cells and control (empty scaffold) treated groups. These findings highlight that although secretomes possess therapeutic potential, their efficacy might be limited compared to cellular therapies. This study contributes to the growing understanding of MSC secretomes, emphasizes the need for further protocol optimization, and offers insights into their potential applications in regenerative medicine.

2023-12-22 | PXD047650 | Pride

Proteomic and phosphoproteomic analysis of ESR1 mutant cells

Project description:Three quarters of all breast cancer cases express the estrogen receptor (ER, ESR1 gene), which promotes tumor growth and constitutes a direct target for endocrine therapies. ESR1 mutations have been implicated in therapy resistance in metastatic breast cancers, in particular to aromatase inhibitors. ESR1 mutations promote constitutive ER activity and affect other signaling pathways, allowing cancer cells to proliferate by employing mechanisms within and outwith direct regulation by the ER. Although subjected to extensive genetic and transcriptomic analyses, understanding of protein alterations remains poorly investigated. Towards this, we employed an integrated mass spectrometry (MS) based proteomic approach to profile the protein and phosphoprotein differences in breast cancer cell lines expressing the frequent Y537N and Y537S ER mutations. Global proteome analysis revealed enrichment of mitotic and immune signaling pathways in ER mutant cells, while phosphoprotein analysis evidenced enriched activity of proliferation associated kinases, in particular CDKs and MTOR. Integration of protein expression and phosphorylation data revealed pathway-dependent discrepancies (motility vs proliferation) that were observed at varying degrees across mutant and wt ER cells. Additionally, protein expression and phosphorylation patterns, while under different regulation, still recapitulated the estrogen-independent phenotype of ER mutant cells.

2024-03-26 | PXD046446 | Pride

Genome-wide maps of XBP1 binding sites in different breast cancer cell lines.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-26 | E-GEOD-49955 | biostudies-arrayexpress

TaqMan microRNA array for microvesicles released from adipose derived stem cells

Project description:Adipose derived stem cells (ASCs) were preconditioned with endothelial differentiation medium (EDM) for four days and then incubated in endothelial basal medium (EBM) supplemented with 1% microvesicle (MV)-free FBS for two days. The conditioned medium was harvested for MV isolation. The small RNA extracted from the MVs was used for microRNA array. qPCR gene expression profiling; Two equal-amount small RNA samples were from two independent experiments.

2014-08-08 | E-GEOD-59811 | biostudies-arrayexpress

Expression data from two breast cancer cell lines

Project description:During cancer progression, carcinoma cells encounter a variety of cytotoxic stresses such as hypoxia, nutrient deprivation, and low pH as a result of inadequate vascularization. To maintain survival and growth in the face of these physiologic stressors, a set of adaptive response pathways are induced. One adaptive pathway well studied in other contexts is the unfolded protein response (UPR), of which XBP1 is an important component. We used microarrays to detect transcriptome profile changes after XBP1 knockdown in breast cancer cell lines, and identify genes and pathways regulated by XBP1, which could help elucidate how XBP1 mediates the adaptive response of breast cancer to cytotoxic stresses. We extracted RNA and hybridized it to Affymetrix microarrays in two breast cancer cell lines (T47D and MDA-MB-231) under treated (hypoxia and glucose deprivation) or untreated conditions with XBP1 knockdown or not.

2013-09-26 | E-GEOD-49953 | biostudies-arrayexpress

Comparative transcriptomic analysis of human epicardial progenitor cells and hiPSC-derived cardiac progenitor cells under hypoxic and normoxic culture conditions

Project description:The adult mammalian heart has been traditionally regarded as a post-mitotic organ with no regenerative capacity. However, this dogma has been refuted by some recent landmark studies. Both cardiac progenitor cells (CPCs) and epicardial progenitor cells (EPDCs) are activated after myocardium infarction and they may influence each other through paracrine mechanisms or direct interactions. Currently, efforts are being made to discover and develop therapeutic molecules to increase the number of CPCs and EPDCs in an infarcted heart. To better understand the characteristics and therapeutic potential of CPCs and EPDCs, as well as the regulatory mechanisms, we performed transcriptomic analysis of human iPSC-derived CPCs and human primary EPDCs and discovered unique gene expression profiles for each cell type. To make sure that the biological and pharmacological findings in cell assays under ambient oxygen conditions are relevant to the in vivo situation, it is important to understand the effect of hypoxia on the behavior, gene expression, and paracrine profiles of the cells. <br>Comparative transcriptomic analysis of human epicardial progenitor cells and hiPSC-derived cardiac progenitor cells was conducted. We performed global transcriptional analysis of two sources of cardiac progenitors, i.e., patient epicardium-derived cells (EPDCs) and cardiac progenitor cells (CPCs) derived from human induced pluripotent stem cells. In addition, we also compared the gene expression profiles of these cells when they were cultured under normoxic- and hypoxic conditions.

2016-06-27 | E-MTAB-4609 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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