Homo sapiens
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PROVIDER: PRJNA352468 | ENA |
REPOSITORIES: ENA
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Project description:Identification of differentially expressed miRNAs between SW480 and SW620 spheroid cultures
| PRJNA352464 | ENA
Project description:Identification of differentially expressed genes between SW480 and SW620 spheroid cultures [mRNA]
| PRJNA352467 | ENA
Project description:Purpose: The goals of this study are to compare the differentially expressed miRNAs between SW480 and SW620. Methods:Total RNA of two samples was used to prepare the miRNA sequencing library.The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq. Results:We found 72 miRNAs were downregulated on the basis of fold-change less than 0.5. However,total 160 miRNAs were upregulated on the basis of fold-change greater than 2. Conclusions: Our study represents the detailed analysis of SW480 and SW620, generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of miRNA content. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2020-01-22 | GSE144002 | GEO
Project description:Microarray-based gene expression analysis identified microRNAs and mRNAs differentially expressed in 5 glioblastoma spheroid cultures upon ATRA treatment. In this study, a set of 5 glioblastoma spheroid cultures was used to acquire microRNA expression profiles, leading to the identification of differentially expressed microRNAs between untreated and ATRA-treated cultures. In this study, a set of 5 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 16,651 transcripts, leading to the identification of differentially expressed genes between untreated and ATRA-treated cultures by Significance Analysis of Microarray data.
2010-07-20 | E-GEOD-17227 | biostudies-arrayexpress
Project description:Metastasis is a complex process involving multiple steps. We were interested in the role of microRNAs (miRNAs) in the process of liver colonization by colorectal cancer cells. We hypothesized that the comparison between non-metastatic versus metastatic isogenic cell line should thus offer valuable insight to the molecular mechanisms involved in developing metastatic behavior. KM12C/KM12SM and SW480/SW620 are probably the best available models of isogenic cell lines differing in metastatic properties for colorectal cancer. Our first goal was to identify miRNAs that contribute to the metastatic traits of the isogenic colorectal cancer cell lines, KM12C/KM12SM and SW480/SW620. Total RNA was extracted from cells using the mirVana kit (Ambion). Total RNA (1 µg) from KM12C and SW480 (poorly metastatic) and KM12SM and SW620 (highly metastatic) cells was used to analyze the global miRNA expression profiling with TaqMan Megaplex human array A (v2.0) and B (v3.0) (Applied Biosystems).
2017-03-01 | GSE86302 | GEO
Project description:Two colon cancer cell lines, SW480 and SW620, were originated from the same patient. The SW480 cell line was derived from a primary lesion, and the SW620 cell line was cultured from a lymph node metastasis with no intervening chemotherapy at a later time. Since these two cell lines are from a single person, it is likely that differences between the two cell lines represent the changes when cancer cells acquire metastatic potential. Thus, this system represents a perfect model for the study of metastatic mechanism. To investigate cancer metastasis associated miRNAs, we detected the miRNA profiles in these two cell lines.
2009-02-20 | E-MEXP-2060 | biostudies-arrayexpress
Project description:Background: Colorectal cancer (CRC) stands as a significant contributor to cancer-related mortality globally. Approximately 90% of cancer mortality is due to distant metastasis. In the context of therapy, response rates can fluctuate significantly with approximately one-third of the patients experiencing relapse following their initial treatment. Owing to its prognostic and therapeutic implications, intratumoral heterogeneity (ITH) presents a considerable challenge in contemporary oncology. In this pre-clinical investigation, we conducted a comprehensive analysis of ITH during the progression of CRC utilizing a single-cell-based spheroid model. Methods: Single cells of the CRC cell lines from a primary colorectal adenocarcinoma (SW480) and a locoregional lymph node metastasis (SW620) were sorted via FACS and cultured into spheroids. Cell culture growth curves were evaluated via microscopy, viability assays were conducted via ATP measurement. A ‘diameter-related metabolic activity’ (DMA) was calculated using the viability and the spheroid diameter. Label-free liquid chromatography mass spectrometry (LC-MS) further assessed ITH in data-independent acquisition mode. Identifying proteins that were most differently expressed between the samples was accomplished through computation and ranking of the fold changes in protein expression data. Chemotherapy response was measured by conducting a viability assay after incubation with 5-Fluorouracil for 72 hours. Results: Single-cell-derived spheroids from both cell lines showed significant differences in morphology, spheroid size, and viability. Subsequently, significant differences in DMA, which could be correlated with aggressive tumor behavior, were observed. Downstream MS-Analysis detected a maximum of 3,954 proteins of which 1,655 were selected for further evaluation. SW620 showed higher proteomic ITH than SW480, which was mediated by distinct pathways. InSW480 cell populations, the implicated pathways comprised tumor suppressor genes, proto-oncogenes, and transcription factors, while SW620 spheroids showed activated pathways of vascularization and the Warburg effect. Furthermore, individual spheroids responded differently to 5-FU chemotherapy showing higher drug resistance in SW620 cells than in SW480 cells. Conclusion: The present study revealed a more pronounced ITH for single-cell-derived spheroids of SW620 regarding spheroid characteristics, proliferation, and proteome activity compared to SW480 spheroids. These findings suggest a prominent involvement of energy metabolism in the metastatic cascade in colorectal cancer models. Further exploration of ITH could provide an important basis for novel biomarker, for personalized tumor therapy and prediction of therapeutic response.
2026-02-02 | PXD053393 | Pride
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
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
Project description:Microarray-based gene expression analysis identified genes differentially expressed in 10 glioblastoma spheroid cultures compared to normal brain. In this study, a set of 10 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 16 441 transcripts, leading to the identification of differentially expressed genes compared to normal brain by Significance Analysis of Microarray dada.
2010-02-12 | E-GEOD-14818 | biostudies-arrayexpress