Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of highly metastatic cell line

ABSTRACT: A prediction of peritoneal recurrence is of significance using metastasis-related biomarker. This work describes a combined analysis of proteome and transcriptome data for biomarker discovery in highly metastatic cell line. We used nano-flow liquid chromatography (LC) linear ion trap time-of-flight mass spectrometry (LIT-TOF MS) and cDNA microarray to identify specific protein differentially expressed between a highly metastatic stomach cancer cell line MKN-45-P and its parental cell line MKN-45. In total, 240 proteins were found to be expressed between the two cell lines. Of these, 75 proteins (31%) and 49 proteins (20%) were only identified from MKN-45-P and MKN-45 respectively. An mRNA expression of 1533 genes was up-regulated in MKN-45-P compared with MKN-45. No close correlation was found between proteomic and transcriptomic analysis. Interestingly, 4 of 240 proteins (1.6%) were involved in the up-regulated mRNA expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE21328 | GEO | 2010/06/01

SECONDARY ACCESSION(S): PRJNA126177

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome analysis of highly metastatic cell line

Project description:A prediction of peritoneal recurrence is of significance using metastasis-related biomarker. This work describes a combined analysis of proteome and transcriptome data for biomarker discovery in highly metastatic cell line. We used nano-flow liquid chromatography (LC) linear ion trap time-of-flight mass spectrometry (LIT-TOF MS) and cDNA microarray to identify specific protein differentially expressed between a highly metastatic stomach cancer cell line MKN-45-P and its parental cell line MKN-45. In total, 240 proteins were found to be expressed between the two cell lines. Of these, 75 proteins (31%) and 49 proteins (20%) were only identified from MKN-45-P and MKN-45 respectively. An mRNA expression of 1533 genes was up-regulated in MKN-45-P compared with MKN-45. No close correlation was found between proteomic and transcriptomic analysis. Interestingly, 4 of 240 proteins (1.6%) were involved in the up-regulated mRNA expression. Comparison analysis of gene expression between highly metastatic gastric cancer cell line MKN-45-P and its parental cell line MKN-45.

2010-06-08 | E-GEOD-21328 | biostudies-arrayexpress

Genome-wide maps in gastric cancer MKN-45 cells with or without the overexpression of transcriptional factor SIX2

Project description:Analysis of MKN-45 cells following SIX2 stable overexpression or not. SIX2 regulates various mRNA expression in MKN-45 cells.Results provide insight into the role of SIX2-involved mechanisms underlying SIX2-mediated effects on gastric cancer stemness.

2024-06-09 | GSE234584 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes Caused by Dexamethasone Treatment in Cancer Cells

Project description:As commonly used drug in clinical, there is little known about the effects of dexamethasone (Dex) on cancer cells. The goals of this study are to explore the transcriptome caused by Dex in cancer cells. Seven cancer cell lines were used in this project, gastric cancer cell lines SGC-7901 and MKN-45, and colorectal cancer cell lines NCIH-747 and RKO, liver cancer cell line SMMC-7721, pancreatic cancer cell line BxPC3, melanoma cell line MV3. After treated by Dex for 48 hours, total RNAs were extracted for next-generation sequencing profiling.

2021-07-12 | GSE134195 | GEO

Quantitative proteomic analysis of gastric cancer cells treated by bifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir.

Project description:MKN-45 cells were treated with PBS, BF-TK, BF/GCV or BF-TK/GCV for 48 h (GCV, 167 µg/ml), respectively. BF-TK (n = 3), BF/GCV (n = 3) or BF-TK/GCV (n = 3) groups were analyzed in triplicate.

2023-10-24 | PXD042044 | Pride

Combinatory RNA sequencing analyses reveal RNA editing-dependent and -independent gene regulation by ADAR1 in gastric cancer

Project description:To investigate the role of ADAR1 in gastric carcinogenesis, RNA sequencing and small RNA sequencing were performed in AGS and MKN-45 cells with stable ADAR1 knock-down. Changed frequencies of editing and messenger RNA (mRNA) and microRNA (miRNA) expression were then identified by bioinformatic analyses.

2018-11-20 | GSE106874 | GEO

Global cellular biological processes governed by MET amplification

Project description:We used microarrays to probe the global programme of gene expression under treatment with c-Met inhibitor and identified distinct classes of up- and down-regulated genes during this process We treated MET addicted EBC-1 and MKN-45 cells with selective c-Met kinase inhibitor SGX-523 at 1uM for 24 and 48 hours, using HCC827 cells with activated c-Met but lacking MET dependency as a negative control

2015-02-12 | E-GEOD-65854 | biostudies-arrayexpress

Effect of knockdown of GRP94 on gene expression of MKN-45 cells

Project description:Anoikis resistance allows cancer cells to avoid death caused by detachment from the extracellular matrix's adhesion, enabling these cells to infiltrate and migrate to regions such as the peritoneum.Glucose-regulated protein 94 (GRP94, alternatively labeled as HSP90B1) is typically stress-induced and is part of the heat shock protein 90 (Hsp90) family.GRP94 is closely tied to cellular resistance to stress, apoptosis, proliferation, invasion, inflammation, and immunity.Our findings indicated that while attached culture didn't impact the apoptosis rate between shGRP94 and shCtrl groups, GRP94 knockdown weakened anoikis resistance, migration, and invasion abilities. Here, we aim to assess the impact of knocking down GRP94 on gene expression in the gastric cancer cell line MKN-45, to further elucidate potential molecular mechanisms by which GRP94 affects the biological characteristics of gastric cancer cells.

2024-07-25 | GSE267811 | GEO

Nucleosome Distribution Data for Methylphenidate Treatment

Project description:Jurkat T-leukemic cells at 0, 15, 45, and 240 minutes post MPH treatment. Chromatin structure depends highly on the position and density of nucleosomes in the genome. The distribution of these nucleosomes likely plays a critical role in all processes for which DNA is the template, including: gene expression, DNA replication, recombination and repair. It has been proposed for more than half a century that although all the cells in a human body contain, essentially, the same genetic material, nucleosomes give access to different areas of the genome effectively giving access to cell-type specific areas of the genome. We hypothesized that alterations in nucleosome distribution might play a role in the MPH stimulated immune response. We measured chromatin structural changes in a human T-cell line (Jurkat T-leukemic) at high temporal resolution after MPH treatment. We mapped the nucleosome distribution at 4 different time points (0, 15, 45, 240 minutes). Nucleosomal DNA sequences were harvested via chromatin cross-linkage, MNase digestion and DNA extraction. Results were gathered by measuring differences in nucleosome distribution between the basal and the treated states at the different time points. We identified changes in nucleosome distribution. Interestingly, these changes in nucleosome distribution were transient, returning to their basal positions. Finally, these changes in nucleosome distribution exhibited different kinetics at different genes. We propose that the changes in nucleosomal distribution help potentiate differences in gene activity. The results allow us to understand the direct affects of MPH on chromatin structure and help reveal certain mechanistic processes by which it performs. Jurkat T-leukemic cells at 0, 15, 45, and 240 minutes post MPH treatment.

2015-06-26 | E-GEOD-70292 | biostudies-arrayexpress

Examination of HMGA2 binding genes in human HMGA2-exogenous overexpressed gastric cancer cells

Project description:HMGA2 significantly increased cell proliferation capacity of gastric cancer in a HMGA2-dependent manner both in vivo and in vitro and we found HMGA2 promoted GC through accelerating S-G2/M phase.To elucidate the underlining mechanism by which HMGA2 induced the change of phenotype in GC cells, we performed ChIP-seq analysis of HMGA2-OE MKN-45 cells with anti-HMGA2 antibody.

2021-08-18 | GSE174442 | GEO

Effect of knockdown of GRP94 on gene expression of MKN-45 cells

Project description:Effect of knockdown of GRP94 on gene expression of MKN-45 cells

| PRJNA1113161 | ENA