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SW480 N-terminal peptide analysis

ABSTRACT: N-terminal peptide analysis of SW480 cell line for Nt-formylation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Shinyeong Ju

LAB HEAD: Cheolju Lee

PROVIDER: PXD039053 | Pride | 2023-07-20

REPOSITORIES: Pride

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			Action	DRS
	200402_SW480_1.mgf	Mgf
	200402_SW480_1.mzML	Mzml
	200402_SW480_1.mzid.gz	Mzid
	200402_SW480_1.raw	Raw
	200402_SW480_1.tsv	Tabular

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Publications

Detection of Nα-terminally formylated native proteins by a pan-N-formyl methionine-specific antibody.

Kim Dasom D Seok Ok-Hee OH Ju Shinyeong S Kim Sang-Yoon SY Kim Jeong-Mok JM Lee Cheolju C Hwang Cheol-Sang CS

The Journal of biological chemistry 20230327 5

N-formyl methionine (fMet)-containing proteins are produced in bacteria, eukaryotic organelles mitochondria and plastids, and even in cytosol. However, Nα-terminally formylated proteins have been poorly characterized because of the lack of appropriate tools to detect fMet independently of downstream proximal sequences. Using a fMet-Gly-Ser-Gly-Cys peptide as an antigen, we generated a pan-fMet-specific rabbit polyclonal antibody called anti-fMet. The raised anti-fMet recognized universally and s ...[more]

PMID: 36990220

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Expression analysis of colorectal cancer cell line SW480 expressing FOXC2

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

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

Expression data from SW480 cells with Gankyrin knockdown

Project description:We performed genome-wide screening using SW480 cells with Gankyrin knockdown on an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin. Transcriptional profiling with samples from SW480 cells that were infected with control or gankyrin shRNA. Two condition experiment: control shRNA (three replicates) and NFIL3 shRNA (three replicates)

2013-02-04 | E-GEOD-44029 | biostudies-arrayexpress

Human SW480 cells: Untreated vs H2O2 Treated

Project description:ChIP-on-chip tilling array comparing untreated human SW480 cells vs SW480 cells treated with 2mM H2O2 for 30min. Exposing cells to the reactive oxygen species, hydrogen peroxide, recruits DNA methyltransferase 1 (DNMT1) to damaged chromatin. DNMT1 becomes part of a complex(es) containing DNMT3B and members of Polycomb Repressive Complex 4. The goal was to determine the effect of hydrogen peroxide treatment on chromatin, including changes in histone modifications and binding patterns of chromatin-associated proteins. [Agilent-014706]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and EZH2. [Agilent-014707]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and EZH2. [Agilent-026595]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Five-mark: SIRT1, gamma-HA2X, DNMT1, DNMT3B, and H3. [Agilent-027811]: Two-condition: untreated SW480 cells (U) vs H2O2 treated SW480 cells (T). Four-mark: H3, 3MeK4H3, AcK16H4, and 3MeK27H3.

2011-12-01 | E-GEOD-32382 | biostudies-arrayexpress

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

SW480 Signaling Hub Inhibition

Project description:In tumor cells, stepwise oncogenic deregulation of signaling cascades induces alterations of cellular morphology and promotes the acquisition of malignant traits. Using a panel of small molecular inhibitors, we established associated gene expression signatures of key signaling hubs. SW480 cells were grown in DMEM, 10% FCS, and treated for 24h with the following inhibitors or with solvent (DMSO): SU5402 (42uM); U0126 (10uM), SP600125 (20uM), LY294002 (20uM)

2011-06-03 | E-GEOD-29689 | biostudies-arrayexpress

mRNA-seq of SW480 USP22 knockdown cells

Project description:This analysis identifies genes which are affected in SW480 cells upon siRNA-mediated USP22 knockdown

2019-12-05 | E-MTAB-8214 | biostudies-arrayexpress

Role of TAZ as mediator of Wnt signaling (SW480)

Project description:To investigate the role of TAZ downstream of the abberrant Wnt signaling in CRC cells, we compared the expression profiles of parental SW480 cells (empty vector) transfected with siControl, siTAZ, sibeta-catenin or reconstituted with wild type APC and transfected with siControl Keywords: expression profiling by array We collected RNA from parental SW480 cells (empty vector) transfected with siControl, siTAZ, sibeta-catenin or from SW480 cells reconstituted with wild type APC and transfected with siControl. Cells were left untreated in normal culturing conditions before harvesting. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Four biological replicas (A, B, C, D) were used for each of the 4 conditions (1: siControl, control cells; 2: siTAZ cells; 3: sibeta-catenin (sibcat) cells; 4.APC reconstituted cells) for a total of 16 samples.

2012-12-21 | E-GEOD-39904 | biostudies-arrayexpress

Exosomal natural antisense transcripts released from colorectal cancer SW480 cells into culture supernatants

Project description:In the present study, natural antisense transcripts (NATs), transcribed from reverse strand deoxynucleic acids (DNAs) of genes, into exosomes released from colorectal cancer SW480 cells were searched using an sense/antisense-custom microarray. SW480 cells were cultured with serum-free RPMI1640 for 48 h. Then, culture media were collected, centrifugated, and filtrated using 0.22-um filters. Exosomes from culture media were collected by ultracentrifugation.

2015-05-19 | E-GEOD-68979 | biostudies-arrayexpress

Diverse effect of WWOX overexpression in SW480 colon cancer cell line.

Project description:The WWOX gene is a tumor suppressor probably involved in regulation of cell cycle and apoptosis and downregulated in variety of cancer types.However, its role in colon cancerogenesis is unknown. The aim of this study was to characterize how WWOX may be involved in colon cancerogenesis or cancer progression, how it influences the basic cancer cell features and modifies cell expression profile.Our observations suggest that in HT29 colon cancer cell line increased expression of WWOX may result in transition of cancer cells into more normal- like colon epithelium phenotype, on the other hand in SW480 WWOX revealed the well-known tumour suppressor properties. However, as the colon cancer is very heterogeneous disease, obtained discrepancies may reflect the known differences between cell lines and cancerogenesis pathway, which they undergone. SW480 colon cancer cells were stably transfected with WWOX cDNA. SW480 cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.

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