Transcription profiling by array of human gastric cancer cell line MC-4 treated with pPeOp against untreated controls
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PROVIDER: PRJNA595163 | ENA |
REPOSITORIES: ENA
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Project description:Microarray analysis was performed to find out differentially expressed genes in pPeOp-treated MC-4 gastric cancer cells.
2019-12-13 | GSE141914 | GEO
Project description:Gastric Cancer proteome analysis for untreated and treated (PTX+RAM) patients
2024-09-18 | PXD050311 | JPOST Repository
Project description:Background: Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium Methylation EPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. Methods: Epigenome-wide DNA methylation in four peripheral blood mononuclear cell samples was profiled by using SureSelectXT Methyl-Seq for MC-seq and EPIC platforms separately. CpG site-based reproducibility of MC-seq was assessed with DNA sample inputs ranging in quantity of high (> 1000ng), medium (300-1000ng), and low (150ng-300ng). To compare the performance of MC-seq and the EPIC arrays, we conducted a Pearson correlation and methylation value difference at each CpG site that was detected by both MC-seq and EPIC. We compared the percentage and counts in each CpG island and gene annotation between MC-seq and the EPIC array. Results: After quality control, an average of 3,708,550 CpG sites per sample was detected by MC-seq with DNA quantity >1000ng. Reproducibility of MC-seq detected CpG sites was high with strong correlation estimates for CpG methylation among samples with high, medium, and low DNA inputs (r > 0.96). The EPIC array captured an average of 846,464 CpG sites per sample. Compared with the EPIC array, MC-seq detected more CpGs in coding regions and CpG islands. Among the 472,540 CpG sites captured by both platforms, methylation of a majority of CpG sites was highly correlated in the same sample (r: 0.98~0.99). However, methylation for a small proportion of CpGs (N=235) differed significantly between the two platforms, with differences in beta values of greater than 0.5. Conclusions: Our results show that MC-seq is an efficient and reliable platform for methylome profiling with a broader coverage of the methylome than the array-based platform. Although methylation measurements in majority of CpGs are highly correlated, a number of CpG sites show large discrepancy between the two platforms, which warrants further investigation and needs cautious interpretation.
2020-06-22 | GSE152922 | GEO
Project description:There is still a big debate about the correlation between melanosis coli (MC) and carcinoma. We used HTA2.0 to investigate the expression changes of lncRNAs and mRNAs in human colonic mucosa with or without MC and try to investigate MC from gene aspect, eventually to demonstrate whether there’s a certain correlation between MC and carcinoma. GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) microarrays were adopted. The expression profile of lncRNAs and mRNA were tested in five colon tissue biopsy specimen of MC patients and five demographically-matched controls.
2016-05-30 | GSE78933 | GEO
Project description:Pseudomonas aeruginosa treated with UV against untreated controls
| PRJEB40577 | ENA
Project description:2',3,5-Trimethoxychalcone (MC-23) triggers apoptosis independently of p53 in MiaPaCa2 cells. To understand the mechanism of action of MC-23, we analysed the gene expression profiles in MiaPaCa2 cells treated with 10 μM MC-23 for 6, 12, or 24 h using the Agilent human 44K oligonucleotide V2 microarray. Out of the 34,127 genes in the array, MC-23 upregulated ~3% and downregulated. Notably, a large number of genes associated with apoptosis (such as BAX, BAK), chaperones (such as HSPA1/HSP70, HSPA5/GRP78/BiP), and the unfolded protein response (such as IRE1α, CHOP/DDIT3/GADD153, XBP1, ATF4, ATF6) were highly up-regulated by MC-23 treatment, suggesting that ER stress is associated with MC-23-induced apoptosis.
2014-01-21 | GSE54225 | GEO
Project description:To explore mechanisms underlying wild-type GISTs, array CGH was performed on 32 gastric GISTs (4 risk groups stratified by tumor size and mitotic counts comprised 8 cases each).
2013-06-14 | GSE47912 | GEO
Project description:Microcystins (MCs) are cyclic hepatotoxins produced worldwide by various species of cyanobacteria. Their structure includes two variable amino acids (AAs) and most of the studies focused on the most toxic variant: the microcystin LR (MC-LR). However, more than 80 MC variants have been described to date. Despite ingestion being the major pathway of human exposure, few in vivo studies have demonstrated macroscopic effects on the gastro-intestinal tract, but no data are available on the affected pathways by several variants on intestinal cells. Here, using a non-selective method, we investigated for the first time the effect of MC-RR and MC-LR on the human intestinal cell line Caco-2 and compared their response at the pangenomic scale. The cells were incubated for 4 hrs or 24 hrs with the same range of sub-lethal concentrations of MC-RR or MC-LR. Low effects were observed for both variants after a short-term exposure. On the contrary, dose-dependent modulations of the genes transcription levels were noticed with MC-RR and MC-LR after 24 hrs. Furthermore, the genomic profiles induced by both variants were similar suggesting a common toxicity mechanism but with higher modulation following MC-LR than MC-RR exposure. However, the functional annotation revealed major differences between the variants effects. Indeed, the well-known MC-LR affected mainly two pathways, the oxidative stress response and the cell cycle regulation, which did not elicit significant alteration following MC-RR exposure. This work is the first comparative description of the MC-LR and MC-RR effects on a human intestinal cell model. It allowed us to suggest differences in the mechanism of toxicity for MC-RR and MC-LR. These results illustrate that the toxicity of MC variants remains a key point for risk assessment.
2012-12-31 | GSE29861 | GEO
Project description:There is still a big debate about the correlation between melanosis coli (MC) and carcinoma. We used HTA2.0 to investigate the expression changes of lncRNAs and mRNAs in human colonic mucosa with or without MC and try to investigate MC from gene aspect, eventually to demonstrate whether thereâs a certain correlation between MC and carcinoma. GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) microarrays were adopted. The expression profile of lncRNAs and mRNA were tested in five colon tissue biopsy specimen of MC patients and five demographically-matched controls. This study recruited a total of five MC patients and five coupled matched controls. All specimens were obtained from colonoscopy. The fresh specimens of colon tissues form MC patients and control patients were washed with RNAase free water and put into RNAlater (Qiagen) immediately and frozen in -80°C. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways.
2016-05-30 | E-GEOD-78933 | biostudies-arrayexpress
Project description:Array CGH analysis was done with 56 primary gastric cancers to elucidate prognostic biomarkers on the BAC basis.
2010-08-10 | GSE15436 | GEO