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TMT-based quantitative proteomic analysis of spheroid cells of endometrial cancer possessing cancer stem cell properties

ABSTRACT: TMT-based quantitative proteomic analysis of spheroid cells of endometrial cancer possessing cancer stem cell properties

PROVIDER: PRJNA922756 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23597570_1.fastq.gz	Fastqsanger.gz
	SRR23597570_2.fastq.gz	Fastqsanger.gz
	SRR23597571_1.fastq.gz	Fastqsanger.gz
	SRR23597571_2.fastq.gz	Fastqsanger.gz
	SRR23597572_1.fastq.gz	Fastqsanger.gz

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TMT-based quantitative proteomic analysis of spheroid cells of endometrial cancer possessing cancer stem cell properties

Project description:RNA-seq of HK2-siRNA transfected to Ishikawa and HEC1A cells to investigate the molecular mechanism of HK2 in endometrial cancer.

2023-01-14 | GSE222599 | GEO

miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MDA-MB-231 cell line.

Project description:cancer spheroid has been widely used as in vitro model of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance. From the miRNA profile, miR-15b, miR-34a, miR-148a, miR-628 and miR-196b were shown to be involved in CSCs-associated signalling pathways in both models of spheroids which highlights the involvement of these miRNAs in maintaining the CSCs features. In addition, unique clusters of miRNAs namely miR-205, miR-181a and miR-204 were found in basal-like spheroid whereas miR-125, miR-760, miR-30c and miR-136 were identified in luminal-like spheroid. Our results highlight the roles of miRNAs as well as providing novel perspectives of the relevant pathways underlying spheroid-enriched CSCs in breast cancer. Keywords: Breast

2016-11-17 | GSE75396 | GEO

miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line

Project description:Intro: Spheroid culture especially on MCF-7 cell has been used as in vitro CSC model for anti-CSC drug discovery. The role of miRNAs in the regulation of mRNA specifically looking at the self-renewal capacity and the drug resistance of the spheroid-enriched CSCs models has not been evaluated. Therefore, a comprehensive profiling of the miRNAs will provide an insight into the regulatory mechanisms associated with breast cancer and CSCs. Methods: Tumour spheroid of MCF-7 was generated and characterised for the biological features and CSCs characteristic comparing to the monolayer parental MCF-7 cells. Differential expression of miRNA between the spheroid and parental cells was evaluated using next generation sequencing (NGS). The differentially expressed miRNAs were then subjected to target genes predictions, followed pathway analyses to better understand the mechanism associated with spheroid-enriched CSCs. Results: Spheroids generated from MCF-7 cell line under serum-free condition were found to be enriched with CSCs characteristics. miRNA-NGS analysis revealed 119 differentially expressed miRNAs between the spheroids and parental, with 24 up-regulated and 94 down-regulated. The gene ontology (GO) analysis showed that the predicted genes of the differentially expressed miRNAs were enriched in various biological processes. Pathway analysis revealed that the differentially expressed miRNAs and their target genes were associated with a variety of KEGG pathways, which could explain the self-renewal capability, and the higher drug resistance in spheroids when compared to parental.

2016-05-10 | GSE68246 | GEO

miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line.

Project description:Intro: Spheroid culture especially on MCF-7 cell has been used as in vitro CSC model for anti-CSC drug discovery. Methods: Tumour spheroid of MCF-7 was generated and characterised for the biological features and CSCs characteristic comparing to the monolayer parental MCF-7 cells. Differential expression of miRNA between the spheroid and parental cells was evaluated using miRNA microarray expressions.

2020-09-20 | GSE68031 | GEO

Effects of spheroid and adherent growth conditions in ovarian cancer

Project description:Purpose: To understand the changes in RNA expression in tumor-initiating cell (TIC) (spheroid) and non-TIC populations (adherent) in ovarian cancer. Methods: OV90 cells were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condition and RNAseq was performed and analysed for differential gene expression between the conditions.

2020-10-03 | GSE158949 | GEO

Phenotypic and microRNA characterisation of the hidden CD24+ cell population in MCF-7 breast cancer 3D spheroid culture

Project description:Introduction: In vitro 3-dimension spheroid culture has been widely used as model to enrich CD44+CD24dim/- cancer stem cells with high ALDH1 activity. However, present of the CD24+ population in the 3D spheroid also requests further attention as this side-population of cells may response differently to drug treatment comparing to the cancer stem cells. Methods: In this study, CD24+ population from the MCF-7 spheroid was sorted and subjected to spheroid formation test, stem cell markers immunofluorescence, invasion/migration test, and microRNA expression profiling. MCF-7 CD24+ cells sorted from primary spheroid reform 3D spheroid after longer period of time associated with dim expression of surface SOX-2, CD44, CD49f and Nanog comparing to the primary spheroid. Results: Remarkably, the MCF-7 CD24+ cells was found with high expression of ALDH1 protein, which subsequently contributed to higher resistant against doxorubicin and cisplatin. MicroRNA profiling has shown that absent of cancer stem cell phenotypes were contributed by the downregulation of major cancer stem cells related pathways including Hedgehog, Wnt and MAPK signalling pathways. Besides, resistance of CD24+ cells was correlated to dyregulation of cell death pathway.

2018-03-12 | GSE95598 | GEO

Analysis of citrullination of extracellular matrix proteins in spheroid cultures of fibroblasts and cancer cells

Project description:Eight different human cancer cell lines were cocultured with human cancer associated fibroblasts (CAF) as spheroid cultures. In another setup UT-SCC-7 cutaneous squamous cell carcinoma cells, together with human skin fibroblasts (SFB) and UT-SCC-2 cells together with gingival fibroblasts (GFB) were cultured as spheroid cocultures. These spheroids were treated with PAD4 or with citrullination buffer only. All spheroids were hypotonically lysed, and the remaining insoluble material was digested to peptides and analysed by LC-MS/MS.

2022-11-21 | PXD033555 | Pride

Effects of spheroid and adherent growth conditions in ovarian cancer

Project description:Effects of spheroid and adherent growth conditions in ovarian cancer

| PRJNA667082 | ENA

A deep insight about the role of hydrogen cynamide in grape bud dormancy release by comparative transcriptomic and proteomic analysis

Project description:Hydrogen cyanamide (HC) is an agrochemical compound frequently used to break bud dormancy in grapevine grown under mild winter conditions all over the world. The present study was carried out to get a better understanding of the molecular mechanism associated with HC to release bud dormancy in grapevine using RNA-seq based transcriptomic and tandem mass tag (TMT) based proteomic analysis.

2019-12-19 | GSE127322 | GEO

Gene expression analysis of glioblastoma spheroid cultures II

Project description:Microarray-based gene expression analysis identified genes differentially expressed in 10 glioblastoma spheroid cultures compared to a non-neoplastic spheroid culture isolated from the bulbus olfactorius In this study, a set of 10 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 17 093 transcripts, leading to the identification of differentially expressed genes compared to a non-neoplastic brain spheroid culture

2010-02-12 | E-GEOD-16666 | biostudies-arrayexpress

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