Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA352467 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Identification of differentially expressed miRNAs between SW480 and SW620 spheroid cultures
| PRJNA352464 | ENA
Project description:Identification of differentially expressed miRNAs between SW480 and SW620 spheroid cultures [miRNA]
| PRJNA352468 | ENA
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: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: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
Project description:As one of the leading causes of cancer deaths worldwide, colorectal cancer (CRC) development is closely associated with the accumulation of both genetic and epigenetic alterations. Many efforts have been made to investigate the role of epigenetic modifications in CRC metastasis. In this work, we present the first quantitative top-down proteomics study focusing on histone proteoforms between metastatic (SW620) and nonmetastatic (SW480) CRC cells to reveal potentially critical histone proteoforms in CRC metastasis. We isolated histone proteins from CRC cells, separated them by sodium dodecyl-sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), recovered each histone protein from the gel, and analyzed them by capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS). A total of 230 histone proteoforms were quantified in SW480 and SW620 cell lines, among which 34 proteoforms were significantly altered in abundance in the metastatic cells, indicating a significant transformation of histone proteoforms during metastasis. We observed a significant increase in abundance of all nine differentially expressed histone H4 proteoforms in metastatic SW620 cells compared to SW480 cells, while differentially expressed proteoforms of other histone proteins display diversified expression patterns. Additionally, two histone H2A proteoforms with a combination of N-terminal acetylation and phosphorylation were upregulated in the metastatic CRC cells. These differentially expressed histone proteoforms could be novel proteoform biomarkers of CRC metastasis.
2025-11-21 | PXD060160 | Pride
Project description:We profiled genome-wide DNA methylation in four cancer cell line, ie SW480-lenti SW480-TET2CD, SW620--lenti and SW620-TET2CD.
2020-07-21 | GSE154734 | GEO
Project description:The differential ribosome-bound lncRNAs between SW620 and SW480 were investigated by RNA-seq.
2020-05-26 | GSE139407 | GEO
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
2010-02-13 | GSE16666 | GEO