Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA148193 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression profiles were generated for eight genes located on chromosome 13 following RNAi to enable the determination of gene specific LOF RNAi signatures in the colorectal cancer cell line SW480.
2013-04-05 | GSE33824 | GEO
Project description:Expression profiles were generated for eight genes located on chromosome 13 following RNAi to enable the determination of gene specific LOF RNAi signatures in the colorectal cancer cell line SW480. Triplicate transfections of SW480 cells were performed using two different siRNA duplexes corresponding to each gene target in 6-well plates using the same protocol scaled 30-fold. RNA was purified 72 hrs after transfection. RNA was also purified from negative control siRNA-transfected cells (AllStar siNegative (siNEG), Qiagen). Reduction in target mRNA levels was confirmed by real-time PCR prior to the array analysis.
2013-04-05 | E-GEOD-33824 | biostudies-arrayexpress
Project description:Despite the growing recognition of the role of the stroma in cancer growth, invasive behavior and metastasis, the exact mechanisms of its participation remain unclear. We have explored the relationships between the epithelial/mesenchymal (E/M) state of colorectal cancer cells, their ability to activate fibroblasts, and the expression of collagen related genes. To this end, we studied (i) co-cultures of colorectal cancer cells with different hybrid E/M states and normal fibroblasts in a collagen matrix and (ii) patient-derived cancer-associated fibroblasts (CAFs). Using RNA-sequencing, we found that the different cancer cells can activate normal fibroblasts, which could form dense collagen networks. The functional enrichment analysis of differentially expressed genes indicates more mesenchymal phenotype and greater motility of SW480 cells compared to HT29 cells. The genes related to collagen biosynthesis and catabolism tend to be more active in SW480 cells rather than HT29 cells. Moreover, LOXL2 and LOXL3 genes, which are necessary for collagen fibril organization, are SW480 specific, which may indicate greater input of this cell line in collagen remodeling compared to HT29 cells. The expression of several CAF marker genes is activated in NFs upon co-cultivation with HT29 and SW480. Interestingly, a more-epithelial cell line HT29 activates the fibroblasts to a greater extent, than does SW480. The co-cultivation of colon cancer cell lines HT29 or SW480 with NFs leads to the activation of collagen biosynthesis and collagen fibril organization genes in NFs. Our findings suggest that the normal fibroblasts, activated by cancer cells, contribute to the organization of the extracellular matrix. Therefore, targeting the ability of cancer cells to activate normal fibroblasts can be considered as a new therapeutic strategy.
2020-10-30 | GSE155343 | GEO
Project description:Two isogenic human colorectal cancer cell lines (primary SW480 cell line and its lymph node metastatic variant SW620 cell line),as an in vitro metastatic model. We have demonstrated that SW620 cell line possesses high metastasis potential and SW480 cell linepossesses low metastatic potential. We want to compare the whole cell microRNAs profiles of two isogenic colorectal cancer cell lines (SW480 and SW620 cell line), to gain an insight into the molecular events of colon cancer metastasis.
2016-08-01 | E-GEOD-72412 | biostudies-arrayexpress
Project description:To validate the suitability of two commonly used colorectal cancer cell lines, DLD1 and SW480, as model systems to study colorectal carcinogenesis, we treated these cell lines with β-catenin siRNA and identified β-catenin target genes using DNA microarrays. The list of identified target genes was compared to previously published β-catenin target genes found in the PubMed and the GEO databases. Based on the large number of β-catenin target genes found to be similarly regulated in DLD1, SW480 and LS174T as well as the large overlap with confirmed β-catenin target genes, we conclude that DLD1 and SW480 colon carcinoma cell lines are suitable model systems to study β-catenin regulated genes and signaling pathways
2013-12-31 | GSE44097 | GEO
Project description:To validate the suitability of two commonly used colorectal cancer cell lines, DLD1 and SW480, as model systems to study colorectal carcinogenesis, we treated these cell lines with beta-catenin siRNA and identified beta-catenin target genes using DNA microarrays. The list of identified target genes was compared to previously published beta-catenin target genes found in the PubMed and the GEO databases. Based on the large number of beta-catenin target genes found to be similarly regulated in DLD1, SW480 and LS174T as well as the large overlap with confirmed β-catenin target genes, we conclude that DLD1 and SW480 colon carcinoma cell lines are suitable model systems to study beta-catenin regulated genes and signaling pathways 12 arrays (2 cell lines, 2 treatments, 3 biological replicates)
2013-12-31 | E-GEOD-44097 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a colorectal cancer cell line SW480 expressing FOXC2, compared to the pBabe control cells. Genes associated with metastasis regulated by FOXC2 in colorectal cancer were analysed. The role of FOXC2 in breast cancer metastasis are further described in Mani SA, Yang J et al. Mesenchyme Forkhead 1 (FOXC2) plays a key role in metastasis and is associated with aggressive basal-like breast cancers. PNAS 2007; 104: 10069-10074 . A six chip study using total RNA recovered from three separate cultures of SW480/pBabe and three separate cultures of SW480/FOXC2. Each chip measures the expression level of 45033 genes from SW480/pBabe or SW480/FOXC2.
2014-07-02 | E-GEOD-58980 | biostudies-arrayexpress
Project description:Two isogenic human colorectal cancer cell lines (primary SW480 cell line and its lymph node metastatic variant SW620 cell line),as an in vitro metastatic model. We have demonstrated that SW620 cell line possesses high metastasis potential and SW480 cell linepossesses low metastatic potential.
2016-08-01 | GSE72412 | GEO
Project description:In this study, we use cancer cell lines to investigate the molecular differences between resistant and responsive colorectal cancer cells. Since the treatment of patients with locally advanced rectal cancers involves chemoradiotherapy (CT/RT), we specifically implemented an in vitro protocol that mimics this clinical setting. We anticipate that this analysis will unveil relevant pathways underlying the resistance of rectal cancers to CT/RT, and enable the identification of novel therapeutic target genes. 12 colorectal cancer (CRC) cell lines were obtained from the ATCC, and cultured in the respective tissue culture medium as recommended by the ATCC: Caco-2, HT-29, LS411N, LS513, LS1034, SW403, SW480, SW620, SW837, SW1116, SW1463, and WiDr. For each cell line, RNA was independently isolated at three different passages, and hybridized to a gene expression array. Accordingly, there are three biological triplicates per cell line. Additionally, SW480 (triplicate), SW837 (triplicate), and Caco-2 (duplicate) were cultured in RPMI.
2011-02-10 | E-GEOD-20298 | biostudies-arrayexpress
Project description:To identify STC2-regulated downstream target genes, we compared the results of RNA-seq analysis between colorectal cancer cells without STC2 (SW480-NC) and cells with STC2 (SW480-STC2).
2019-07-02 | GSE116521 | GEO