MiRNA data from melanoma-derived exosomes and melanoma cell lines
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ABSTRACT:
PROVIDER: PRJNA514998 | ENA |
REPOSITORIES: ENA
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Project description:Identify miRNAs enriched or overexpressed in melanoma-derived exosomes compared to melanoma cells. We analyzed the 2,578 human miRNAs located in the array according to two ways. The first one identified the differentially expressed miRNAs between melanoma-derived exosomes and their parent cells. In this way, we found 198 miRNAs up-regulated in melanoma cell lines compared to their exosomes and 206 miRNAs up-regulated in exosomes compared to their donor cells. The second way of analysis identifies the most expressed miRNAs in the melanoma-derived exosomes without assumption about their expression in parent cells. We defined two criteria; the first one is a RMA (Robust Multi-Array Average, a good alternative to gene expression value) above 5, corresponding to the mean expression level of the array and a SD ≤ 0.2 between all samples to discover miRNAs expressed uniformly between melanoma-derived exosomes M113 and M117. We identified 44 miRNAs under these criteria.
2019-01-15 | GSE125030 | GEO
Project description:RNA data from melanoma-derived exosomes and melanoma cell lines
| PRJNA590140 | ENA
Project description:characterize lncRNA and mRNA present in melanoma-derived exosomes
2020-12-31 | GSE140531 | GEO
Project description:Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression. Total RNA from cells and exosomes were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines. RNA was quantified using Nanodrop ND-1000. The integrity of these total RNAs was assessed using Agilent 2100 Bioanalyzer. Total high-quality RNA was labelled. The miRNA array profiling was performed by using the Affymetrix GeneChip miRNA Array 1.0. Two different RNA preparations from two cell lines and their exosomes were used, except that only one RNA preparation was used for HEMa-LP exosome miRNA array. Due to the limited number of passages (approximately 10), adequate exosomal RNA and proteins from HEMa-LP cells for multiple analyses was not available.
2012-10-10 | E-GEOD-35387 | biostudies-arrayexpress
Project description:Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression. Total RNA from cells and exosomes were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines. RNA was quantified using Nanodrop ND-1000. The integrity of these total RNAs was assessed using Agilent 2100 Bioanalyzer. Total high-quality RNA was converted to cDNA, transcribed and labelled, and then hybridized to human HG-U133 plus 2 arrays (Affymetrix) then scanned according to the standard protocol recommended by Affymetrix. Two different RNA preparations from two cell lines and their exosomes were used.
2012-10-10 | E-GEOD-35388 | biostudies-arrayexpress
Project description:Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression.
2012-10-10 | GSE35388 | GEO
Project description:Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression.
2012-10-10 | GSE35387 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE35387: Expression data from normal melanocyte, melanoma cells and their exosomes (microRNA) GSE35388: Expression data from normal melanocyte, melanoma cells and their exosomes (mRNA) Refer to individual Series
2012-10-10 | E-GEOD-35389 | biostudies-arrayexpress
Project description:Exosomes were isolated by differential centrifugation from the fusion negative human embryonal rhabdomyosarcoma (ERMS) cell lines (JR1, Rh36, and RD) and fusion positive alveolar RMS (ARMS) cell lines (Rh30 and Rh41) and characterized by western blot for exosomal markers. miRNA content of the RMS-derived exosomes was determined using the Affymetrix GeneChip miRNA 3.0 array and analyzed to specify differentially deregulated (either enriched or depleted) miRNA relative to cellular miRNA from the respective ERMS and ARMS cell lines. Characterization of the miRNA content of RMS exosome is needed to better understand the mechanism by which these particles exert their physiologic effects, notably on proliferation, migration, invasion, and metastasis.
2016-12-01 | E-MTAB-5321 | biostudies-arrayexpress
Project description:Over the last decades, exosomes have received increasing attention due to their involvement in numerous pathologies including cancer. Tumor-derived exosomes and exosomes derived from the tumor microenvironment are implicated in multiple mechanisms that support disease progression such as the escape of malignant cells from immunosurveillance, tumor cell growth, tumor angiogenesis, preparation of a pre-metastatic niche and remodeling of the extracellular matrix, thereby promoting dissemination and metastasis. Here, we performed protein expression phenotyping of exosomes derived from different invasive and proliferative melanoma cell lines (n=8) to provide a solid framework of gene expression programs, which - in a clinical setting - would be useful for prognosis and may also predict treatment response. Cell line characteristics have been published previously (Wenzina et al.,2020). Having identified a set of differentially expressed proteins in proliferative and invasive melanoma cell lines, we correlated them to the protein composition of plasma exosomes from melanoma patients pre and post immunotherapy treatment (n=7) as well as healthy controls (n=5).
2022-07-14 | PXD025475 | Pride