Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ENRICHMENT IN C-KIT IMPROVES STEM CELL POTENTIAL OF FOETAL HUMAN AMNIOTIC FLUID CELLS: CHARACTERIZATION FROM SINGLE CELL ANALYSIS TO THE SECRETOME EFFECT [Bulk RNA-Seq]

ABSTRACT: Human amniotic fluid cells (hAFSCs) are a fascinating foetal cell-type that have important stem cell characteristics, since described as broadly multipotent immature cells with high self-renewal and no tumorigenic properties. However, amniotic fluid contains a heterogeneous population of amniocytes, from totally differentiated or progenitor cells to highly multipotent stem cells. There is no single approach to isolating the stem cell component, but the selection of a subpopulation of hAFSCs expressing c-Kit (or CD117) is widely employed, while a deep characterization of the two populations is still lacking. Here we performed single-cell and bulk RNAseq analysis to compare the gene expression profiles of adherent amniotic fluid cells and their subpopulation c-Kit+. Information deriving from this high throughput technology on the transcriptome was then confirmed for specific targets with protein expression experiments and functional analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE219024 | GEO | 2023/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

ENRICHMENT IN C-KIT IMPROVES STEM CELL POTENTIAL OF FOETAL HUMAN AMNIOTIC FLUID CELLS: CHARACTERIZATION FROM SINGLE CELL ANALYSIS TO THE SECRETOME EFFECT [scRNA-Seq]

Project description:Human amniotic fluid cells (hAFSCs) are a fascinating foetal cell-type that have important stem cell characteristics, since described as broadly multipotent immature cells with high self-renewal and no tumorigenic properties. However, amniotic fluid contains a heterogeneous population of amniocytes, from totally differentiated or progenitor cells to highly multipotent stem cells. There is no single approach to isolating the stem cell component, but the selection of a subpopulation of hAFSCs expressing c-Kit (or CD117) is widely employed, while a deep characterization of the two populations is still lacking. Here we performed single-cell and bulk RNAseq analysis to compare the gene expression profiles of adherent amniotic fluid cells and their subpopulation c-Kit+. Information deriving from this high throughput technology on the transcriptome was then confirmed for specific targets with protein expression experiments and functional analysis.

2023-03-01 | GSE219023 | GEO

Amniotic fluid cardiomyocytes

Project description:Microarray data comparison of amniocytes, amniotic fluid-iPSCs, and cardiomyocyte derivatives

2016-01-20 | GSE76965 | GEO

Amniotic fluid-derived cells: genome-wide expression in early and late cultures

Project description:Amniotic fluid stem cells (AFSCs) are of interest in regenerative medicine as a non-controversial and potentially 'abundant' source of stem cells. Progress has been made in understanding amniotic fluid stem cell biology, and amniotic fluid-derived cells have been induced to form neurons, osteoblasts, muscle cells, and others. Our study evaluates change in the genome-wide expression profile of amniotic fluid stem cells during in-vitro culture, using Affymetrix U133 Plus 2.0 microarray chips. We found that only 3.08% of gene probes were differentially expressed from early to late passage of AFSC culture. The differentially expressed genes were related to biological processes or cellular function - including transcription factors, protein kinases, and cytokines/growth factors. Other gene-sets of interest were oncogenes and tumor suppressor genes, which were a very small number of genes. We further analyzed the gene sets of interest using NIH DAVID and GSEA bioinformatics databases for gene annotations analysis. Applying false discovery rate correction, there was no significant difference in the genome-wide expression profiling between early and late passage. AFSCs maintain their genome-wide expression profile during in-vitro culture. Amniotic fluid-derived c-kit-positive cells were maintained in stem cell culture and genome-wide expression changes were studied and compared between early passage and late passage in culture.

2012-08-02 | E-GEOD-39839 | biostudies-arrayexpress

Single-cell transcriptomics of cultured human amniotic fluid cells from the second trimester reveals their heterogeneity

Project description:Amniotic fluid has been proposed as an easily available source of cells for numerous applications in regenerative medicine and tissue engineering. The use of amniotic fluid cells in biomedical applications necessitates their unequivocal characterization; however, the exact cellular composition of amniotic fluid and the precise tissue origins of these cells remain largely unclear. Using cells cultured from human amniotic fluid of the second trimester from a healthy fetus and fetuses with spina bifida aperta, we have performed single-cell RNA sequencing to characterize the tissue origin and marker expression of cultured amniotic fluid cells at the single-cell level. Our analysis identified nine different cell types of stromal, epithelial and immune cell phenotype, and from various fetal tissue origins, demonstrating the heterogeneity of the cultured amniotic fluid cell population at single-cell resolution. Further, our data question the presence of pluripotent stem cell populations in cultured AF, and provide a comprehensive list of markers for the characterization of its various progenitor and terminally differentiated cell types. Our study highlights the relevance of single-cell analysis approaches for the characterization of amniotic fluid cells in order to harness their full potential in biomedical research and clinical applications.

2023-07-05 | GSE206696 | GEO

Transcription profiling of human fetuses using oligonucleotide microarray analysis of fetal mRNA isolated from amniocytes to investigate the genetic background of the polygenic neural tube defect Spina bifida

Project description:In polygenic disorders we do not know exactly, how many genes are involved in the pathomechanism, but the analysis of fetal gene expression can get us closer to the solution. In our study we were searching for the genetic background of the polygenic neural tube defect, which is the second most common birth defect in the world (1 in 1000 live births). Our data revealed novel candidate genes, like SLAP, LST1 and BENE, which can play an important role in the pathogenesis of neural tube defects. We created a data warehouse from the results, suitable for further analysis. This study also demonstrates that a routinely collected amount of amniotic fluid (as small as 6 mL) is enough to successfully hybridize isolated RNA to expression arrays, making the ability to use the technique from normally collected amniotic fluid samples. Experiment Overall Design: We report an in vivo study in living human fetuses using oligonucleotide microarray analysis of fetal mRNA isolated from amniocytes, which were collected by amniocentesis. RNA was successfully isolated, amplified, labeled, and hybridized to whole-genome Affymetrix transcript arrays.

2009-04-29 | E-GEOD-4182 | biostudies-arrayexpress

Valproic Acid Confers Functional Pluripotency to Human Amniotic Fluid Stem Cells in a Transgene-free Approach

Project description:Induced pluripotent stem cells (iPSCs) with potential for therapeutic applications can be derived from somatic cells via ectopic expression of a set of limited and defined transcription factors. However, due to risks of random integration of the reprogramming transgenes into the host genome, the low efficiency of the process, and the potential risk of virally induced tumorigenicity, alternative methods have been developed to generate pluripotent cells using nonintegrating systems, albeit with limited success. Here, we show that c-KIT+ human first-trimester amniotic fluid stem cells (AFSCs) can be fully reprogrammed to pluripotency without ectopic factors, by culture on Matrigel in human embryonic stem cell (hESC) medium supplemented with the histone deacetylase inhibitor (HDACi) valproic acid (VPA). The cells share 82% transcriptome identity with hESCs and are capable of forming embryoid bodies (EBs) in vitro and teratomas in vivo. After long-term expansion, they maintain genetic stability, protein level expression of key pluripotency factors, high cell-division kinetics, telomerase activity, repression of X-inactivation, and capacity to differentiate into lineages of the three germ layers, such as definitive endoderm, hepatocytes, bone, fat, cartilage, neurons, and oligodendrocytes. We conclude that AFSC can be utilized for cell banking of patient-specific pluripotent cells for potential applications in allogeneic cellular replacement therapies, pharmaceutical screening, and disease modeling. Total RNA obtained from mid gestation human amniotic fluid cells (AFSCs/2nd trimester AFSCs), early gestation human amniotic fluid cells (eAFSCs/1st trimester AFSCs) and human embryonic stem cells (hESCs) as described in the corresponding Materials and Methods sections.

2012-07-23 | E-GEOD-26940 | biostudies-arrayexpress

Amniotic fluid-derived cells: genome-wide expression in early and late cultures

2012-08-03 | GSE39839 | GEO

Expression data from human amniotic fluid-derived stem cells (AFSC) treated with ethanol

Project description:The effects of ethanol may vary from induction of apoptosis to the inhibition of proliferation, differentiation, migration or other function. The complex and diverse response of fetal cells to ethanol has prompted us to use a bioinformatics approach to study the effect of ethanol on fetal stem cells derived from the amniotic fluid-derived (AFSC). To characterize the global response of human AFSC to ethanol, gene expression profiles of AFSC treated with or without 100mM ethanol for 48 hours were analyzed. Keywords: stem cells, amniotic fluid-derived stem cells, ethanol, alcohol

2009-09-30 | GSE13569 | GEO

ENRICHMENT IN C-KIT IMPROVES STEM CELL POTENTIAL OF FOETAL HUMAN AMNIOTIC FLUID CELLS: CHARACTERIZATION FROM SINGLE CELL ANALYSIS TO THE SECRETOME EFFECT

Project description:ENRICHMENT IN C-KIT IMPROVES STEM CELL POTENTIAL OF FOETAL HUMAN AMNIOTIC FLUID CELLS: CHARACTERIZATION FROM SINGLE CELL ANALYSIS TO THE SECRETOME EFFECT

| PRJNA906601 | ENA

Global Gene Expression Analysis of Term Amniotic Fluid Cell-Free Fetal RNA

Project description:The objective of this study was to identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants. There were 2,871 significantly differentially regulated genes. In term amniotic fluid, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts as compared with brain and embryonic neural cells in the second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation such as immune function, digestion, respiration, carbohydrate metabolism, and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term amniotic fluid. This was a prospective whole genome microarray study comparing eight amniotic fluid samples collected from eight women at term who underwent prelabor cesarean delivery and eight second-trimester amniotic fluid samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second-trimester samples. Pathways analysis software identified physiologic systems, molecular and cellular functions, and upstream regulators that were significantly overrepresented in term amniotic fluid.

2013-04-23 | E-GEOD-46286 | 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