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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genes regulated by Sox2 in colorectal cancer cell line

ABSTRACT: Knockdown of Sox2 in SW620 colorectal cancer cells decrease their growth rates in vitro and in vivo in xenograft models. We used microarrays to detail the global programme of gene expression in Sox2 Knockdown sw620 cells compared with mock knockdown sw620 cells Sox2 knockdown sw620 cells and and mock knockdown sw620 cells were cultured in RPMI 1640 cell culture media for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes regulated by Sox2 in colorectal cell lines and end (T4) of gastrulation.

ORGANISM(S): Homo sapiens

SUBMITTER: Biaoyang Lin

PROVIDER: E-GEOD-20689 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genes regulated by Sox2 in colorectal cancer cell line

Project description:Knockdown of Sox2 in SW620 colorectal cancer cells decrease their growth rates in vitro and in vivo in xenograft models. We used microarrays to detail the global programme of gene expression in Sox2 Knockdown sw620 cells compared with mock knockdown sw620 cells

2011-03-01 | GSE20689 | GEO

Genes regulated by Sox2 in glioma cancer cell line

Project description:Knockdown of Sox2 in LN229 gliomal cancer cells decrease their growth rates in vitro. We used microarrays to detail the global programme of gene expression in Sox2 Knockdown LN229 cells compared with mock knockdown LN229 cells Sox2 knockdown LN229 cells and and mock knockdown LN229 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on Applied Biosystems Human Genome Survey Microarrays . We sought to obtain the genes regulated by Sox2 in glioma cell line.

2011-01-10 | E-GEOD-23838 | biostudies-arrayexpress

MicroRNA expression profile between human colorectal cancer SW480 and SW620 cell line

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

Transcription profiling by array of human colorectal cancer SW620 cells upon MSX1 depletion.

Project description:The first step in the development of human colorectal cancer (CRC) is the aberrant hyperactivation of the Wnt signaling pathway, predominantly caused by inactivating mutations in the adenomatous polyposis coli (APC) gene encoding an essential tumor suppressor. In order to identify genes affected by Apc loss, expression profiling of intestinal epithelium isolated from mice harboring the conditional allele of the gene was performed. The gene encoding transcriptional factor msh homeobox 1 (Msx1) displayed robust upregulation upon Apc inactivation. Subsequently, the expression pattern of human MSX1 was examined in a collection of colonic tumors. The MSX1 mRNA level was increased in all types of human intestinal neoplasia tested. In order to identify genes affected by MSX1 loss, expression profiling of human colorectal cancer cells SW620 upon MSX1 gene depletion was performed.

2019-11-01 | E-MTAB-6928 | biostudies-arrayexpress

mRNA expression after knockdowwn of UICLM in SW620 cells

Project description:The purpose of this study is to identify the disregulated mRNAs after knockdown of UICLM (up-regulated in colorectal cancer liver metastasis, accession number: NR_033841) in SW620 cells. A total of 188 mRNAs were identified to be differentially expressed after knockdown of UICLM in SW620 cells

2017-07-11 | GSE101081 | GEO

High-throughput mass spectrometry analysis of N-glycans and protein markers after FUT8 knockdown in the syngeneic SW480/SW620 colorectal cancer cell model

Project description:MS analysis of proteins from FUT8-knockdown SW480 and SW620 colorectal cancer cells

2024-03-21 | PXD050012 | Pride

TET2 binding protein of human colon cancer cell SW480-SW620

Project description:This project was aimed to identify proteins interatcted with TET2 and the differences between SW480 and SW620.

2023-10-24 | PXD020080 | Pride

Genes regulated by Sox2 in glioma cancer cell line

2011-01-10 | GSE23838 | GEO

Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins in Colorectal Cancer Metastasis

Project description:Epitranscriptomic reader, writer and eraser (RWE) proteins are involved in the recognition, installation, and removal, respectively, of chemical modifications in RNA, and aberrant expressions of some of these proteins were found to be associated with cancer initiation and progression. Here, we our recently established parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labelling by amino acids in cell culture (SILAC), to investigate the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells (i.e., SW480/SW620) derived from the same patient. We were able to detect 113 non-redundant epitranscriptomic RWE proteins in these two lines of cells. We found that 48 and 5 proteins were respectively up- and down-regulated by at least 1.5-fold in SW620 over SW480 cells. Particularly, NAT10, HNRNPC, and DKC1 were markedly up-regulated, and their potential roles in driving CRC metastasis were supported by recent studies. Interrogation of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data revealed that the elevated expressions of these and other RWE proteins are also accompanied with CRC initiation, suggesting the roles of these proteins in both the initiation and metastatic transformation of CRC. It can be envisaged that the established PRM method can be further utilized to examine the roles of epitranscriptomic RWE proteins in the metastatic transformations of other types of cancer.

2022-08-15 | PXD030907 | Pride

Comparison of gene expression between CD133+ and CD133- SW620 human colon cancer cells

Project description:CD133 has been widely used for identification and isolation of cancer stem cells in tumors although its role as a marker for cancer stem cell is still controversial . We isolated the CD133+ and CD133- cells from SW620 human colon cancer cell line and compared their biological characteristics, such as tumorigenicity,drug sensitivity, etc. Our study revealed that CD133+ SW620 cells were more tumorigenic and resistant to anti-cancer drugs. Correspondingly, they displayed different gene expression profile. However, it was observed that CD133- cells and CD133+ cells could mutually convert, indicating that CD133 expression was under dynamic and reversible regulations which might impose significant infulence on cells behaviors. Thus, our data challenge the role of CD133 as a marker for cancer stem cell. There are two populations with distinct expression of CD133 in SW620 human colon cancer cell line. Microarray assays were employed to investigate the differentially expressed genes between the two populations, which may possess different tumorigenetic potential and sensitivity to anti-cancer drugs. CD133+ and CD133- cells were isolated from human colon cancer SW620 cell line by magnetic cell sorting system. The clones from sorted CD133+ or CD133- populations were established. Clone cells were expanded and were further purified by using CD133 cell isolation kit before microarray assays.

2010-07-29 | E-GEOD-23295 | biostudies-arrayexpress

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