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Genome wide microRNA methylome in oral cancer: searching for biomarkers in tobacco users along with possible association with patient’s survival

ABSTRACT: Genome wide microRNA methylome in oral cancer: searching for biomarkers in tobacco users along with possible association with patient’s survival

PROVIDER: PRJNA487627 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7749810.fastq.gz	Fastqsanger.gz
	SRR7749820.fastq.gz	Fastqsanger.gz
	SRR7749830.fastq.gz	Fastqsanger.gz
	SRR7749840.fastq.gz	Fastqsanger.gz
	SRR7749811.fastq.gz	Fastqsanger.gz

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Genome wide microRNA methylome in oral cancer: searching for biomarkers in tobacco users along with possible association with patient’s survival

Project description:We performed reduced representative bisulfite sequencing (RRBS) data on 16 pairs of tumor and adjacent normal tissues from oral squamous cell carcinoma patients to identify methylated biomarkers for disease identification

2021-05-31 | GSE118991 | GEO

Expression data of skeletal muscle from HRT users and non-users

Project description:Modification of Gene Expression of Skeletal Muscle in Response to postmenopause with or without Hormone Replacement Therapy. Even though menopause is often accompanied with first signs of age-associated changes in muscle structure and function, the effects of hormone replacement therapy (HRT) or menopause-related decline in estrogen production in the muscles of postmenopausal women is not well understood. We have used a randomized double-blinded study design together with an explorative microarray experiment to characterize possible effects of continuous, combined HRT and estrogen deprivation on the skeletal muscle of fifteen early postmenopausal women from which 10 used HRT and 5 used placebo for 12-months in a douple-blinded design. Keywords: time course analysis from HRT users and non-users

2007-11-12 | GSE6348 | GEO

Expression data of skeletal muscle from HRT users and non-users

2007-11-12 | E-GEOD-6348 | biostudies-arrayexpress

Comparative Proteomic Analysis of Saliva from Chewing Tobacco Users and Oral Cancer Patients Reveals Shared Biomarkers

Project description:Objectives: The aim of this study was to investigate the salivary proteomic profile of smokeless tobacco users in comparison to non-smokers using LC-MS/MS and to investigate the biological changes associated with smokeless tobacco use and oral cancer. Materials & Methods: Saliva samples of 65 participants were collected and divided into three groups: control (25 participants) , smokeless tobacco users group (25 participant), and oral cancer group (15 participant). The mean ages of the control participants, smokeless tobacco users, and oral cancer patients were 37.08 years, 37.8 years, and 52 years, respectively. The saliva samples were then prepared for LC-MS/MS analysis through in-solution digestion. The raw data files were processed using MaxQuant 2.1.0.0 with the human canonical proteome database. Results: The analysis revealed that 343 protein groups exhibited significantly altered abundance in the saliva samples. Among these, 43 out of 51 dysregulated proteins in the smokeless tobacco group were also dysregulated in the oral cancer group. Notably, Apolipoprotein A1 (ApoA1) and Pon1 were found to be significantly increased in both smokeless tobacco users and oral cancer patients. Furthermore, six out of the 20 most significantly altered proteins were mitochondrial proteins, and all of them were decreased relative to controls in both smokeless tobacco users and cancer samples.

2025-11-17 | PXD045926 | Pride

TestChip Expression data of skeletal muscle from of HRT users and non-users

Project description:Modification of Gene Expression of Skeletal Muscle in Response to postmenopause with or without Hormone Replacement Therapy. Test samples randomly selected from a larger study in order to verify the validity of microarray experiment. Keywords: time course analysis from HRT users and non-users

2007-11-19 | GSE6378 | GEO

Abnormal expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users

Project description:Exposure to electronic cigarette (e-cigarette) aerosol has been linked to a number of health concerns, including DNA damage, elevated oxidative stress, release of inflammatory cytokine, and dysfunctions in epithelial barriers. However, little is known about the effect of exclusive e-cigarette use on expression profiles of exosomal miRNAs, which play critical regulatory roles in many inflammatory responses and disease process including cancer. We aim to compare the exosomal microRNAs expression profile between exclusive e-cigarette users and normal controls without any tobacco product use (non-users). Using blood and urine samples from exclusive e-cigarette users and non-users in the Population Assessment of Tobacco and Health (PATH) Wave 1 study (2013-2014), we examined exosomal microRNAs expression levels through Illumina NextSeq 500/550 sequencing. We identified microRNAs that have significantly higher expression levels in exclusive e-cigarette users than non-users. Gene enrichment analysis of these significant exosomal microRNAs showed their involvement in cancer related pathways, which might indicate a potential elevated risk of cancer among exclusive e-cigarette users.

2024-07-10 | GSE253603 | GEO

Mouthwash samples collected from vape users

Project description:Mouthwash samples collected from vape users Metagenome

| PRJNA795488 | ENA

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced association tandem mass spectrometry and predicted spectral library searching

Project description:Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a novel computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods 2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem. 2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer- predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC/MS. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis

2016-08-17 | PXD002803 | Pride

Dopamine-regulated biomarkers in peripheral blood of HIV+ Methamphetamine users

Project description:HIV and Methamphetamine study - Translational Methamphetamine AIDS Research Center - Dopamine-regulated inflammatory biomarkers A digital transcript panel was custom-made based on Hs_NeuroPath_v1 (Nanostring) to accommodate dopamine-regulated inflammatory genes that were previously identified in vitro, and hypothesized to cluster HIV+ Methamphetamine users.

2024-07-31 | GSE273630 | GEO

Peripheral blood RNA expression profiling in illicit methcathinone users reveals effect on immune system

Project description:Methcathinone (ephedrone) is relatively easily accessible for abuse. Its users develop an extrapyramidal syndrome and it is not known if this is caused by methcathinone itself, by side-ingredients (manganese), or both. In the present study we aimed to clarify molecular mechanisms underlying this condition. We used microarrays to analyze whole genome gene expression patterns of peripheral blood from 20 methcathinone users and 20 matched controls. Gene expression profile data were analyzed by Bayesian modelling and functional annotation. Of 28,869 genes on the microarrays, 326 showed statistically significant differential expression with FDR adjusted p-values below 0.05. Quantitative RT-PCR confirmed differential expression for the most of the genes selected for validation. Functional annotation and network analysis indicated activation of a gene network that included immunological disease, cellular movement and cardiovascular disease functions (enrichment score 42). As HIV and HCV infections were confounding factors, we performed additional stratification of patients. A similar functional activation of the “immunological disease” category was evident when we compared patients according to injection status (past versus current users, balanced for HIV and HCV infection). However, this difference was not large therefore the major effect was related to the HIV status of the patients. Mn-methcathinone abusers have blood RNA expression patterns that mostly reflect their HIV and HCV infections. However, despite the strong confounding effect from infection, some modest drug abuse effects on gene expression were detected. 40 samples, 20 healthy volunteers and 20 illicit methcathinone users

2011-04-19 | E-GEOD-28686 | biostudies-arrayexpress

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