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Transcriptome profiles derived from parallel venipuncture, dried blood spot (DBS), and saliva samples

ABSTRACT: Comparison of transcript abundance estimates derived from DBS vs saliva vs gold standard peripheral blood mononuclear cell (PBMC) samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE79269 | GEO | 2016/07/27

SECONDARY ACCESSION(S): PRJNA315336

REPOSITORIES: GEO

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Transcriptome profiles derived from parallel venipuncture, dried blood spot (DBS), and saliva samples

Project description:Comparison of transcript abundance estimates derived from DBS vs saliva vs gold standard peripheral blood mononuclear cell (PBMC) samples. Gene expression profiling was conducted using parallel collection and assay of venipuncture blood samples (PBMC), DBS samples, and saliva. Data come from 58 community dwelling adults recruited from the Los Angeles metropolitan area. Analyzed data include basic demographic characteristics (age, sex, race/ethnicity) and body mass index (BMI) as well as RNA indicators of major leukocyte subset prevalence (i.e., estimated abundance of mRNA for CD3, CD4, CD8, CD19, FCGR3A/CD16, NCAM1/CD56, and CD14; all provided here as log2-transformed values of normalized gene expression data). Categorial variables were coded 0=no/absent and 1=yes/present.

2016-07-27 | E-GEOD-79269 | biostudies-arrayexpress

Peripheral blood transcriptome profiles derived from parallel venipuncture (PAXgene and mononuclear cell; PBMC) and dried blood spot (DBS) samples.

Project description:Comparison of transcript abundance estimates and bioinformatic inferences derived from DBS vs PAXgene vs peripheral blood mononuclear cell (PBMC) samples.

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Peripheral blood transcriptome profiles derived from parallel venipuncture (PAXgene and mononuclear cell; PBMC) and dried blood spot (DBS) samples.

Project description:Comparison of transcript abundance estimates and bioinformatic inferences derived from DBS vs PAXgene vs peripheral blood mononuclear cell (PBMC) samples. Gene expression profiling was conducted using parallel collection and assay of venipuncture samples (PAXgene and PBMC) and DBS samples. Data come from 83 community dwelling adults recruited from the Chicago metropolitan area. In addition to basic demographic characteristics (age, sex, race/ethnicity), participants were also assessed on health-related characteristics (body mass index/BMI; history of smoking or heavy alchol consumption), and educational attainment (z-score transformed). Categorial variables were coded 0=no/absent and 1=yes/present.

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High Field Asymmetric Waveform Ion Mobility Spectrometry in Non-targeted Bottom-up Proteomics of Dried Blood Spot

Project description:Dried Blood Spots samples are a rich source of proteins and have therefore great potential for proteomics biomarker discovery studies. Only a few articles have used DBS samples for non-targeted bottom-up protein analysis, probably due to the complexity of the DBS samples. Gas-phase separation by ion mobility spectrometry such as Field Asymmetric Waveform Ion Mobility (FAIMS) could be useful in analysis of DBS samples as FAIMS has previously shown to be advantageous for bottom-up protein analysis of complex samples. The aim of this project was therefore to evaluate FAIMS in non-targeted analysis of Dried Blood Spots.

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Evaluation of suitability of dried saliva spots for in-depth proteome analyses of clinical applications

Project description:We performed a single-shot DIA-MS proteome analysis of dried saliva spots (DSS) to investigate whether it provides a platform to complement the dried blood spot (DBS) data.

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Integrating Hepatitis C Screening With Dried Blood Spot Testing Into Colorectal Cancer Screening

Project description:The main purpose of the study is to compare the acceptance and viability of three strategies aimed to screen hepatitis C virus (HCV) infection in a birth cohort by: a) invitation letter offering HCV screening with dried blood spot (DBS) testing at the primary care center, b) invitation letter offering both HCV and colorectal cancer (CCR) screening with faecal occult test (FOT) at the primary care center, and c) invitation letter offering self-collected screening at home for HCV and CCR.

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Evaluation of suitability of dried saliva spots for in-depth proteome analyses of clinical applications - Additional file

Project description:We performed a single-shot DIA-MS proteome analysis of dried saliva spots (DSS) to investigate whether it provides a platform to complement the dried blood spot (DBS) data.

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Project description:We compared the transcriptomic content of salivary exosomes vs. whole saliva via microarray (Affymetrix HU133 plus 2.0).

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