Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

NCounter analysis of mRNAs associated with occupational benzene exposure using a Nanostring custom assay

ABSTRACT: nCounter analysis of mRNAs associated with occupational benzene exposure using a Nanostring custom assay

PROVIDER: PRJNA489476 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

nCounter analysis of mRNAs associated with occupational benzene exposure using a Nanostring custom assay

Project description:Previously, using microarrays and mRNA-Sequencing (mRNA-Seq) we found that occupational exposure to a range of benzene levels perturbed gene expression in peripheral blood mononuclear cells. In the current study, we sought to identify gene expression biomarkers predictive of benzene exposure below 1 part per million (ppm), the occupational standard in the U.S. First, we used the nCounter platform to validate altered expression of 30 genes in 33 unexposed controls and 57 subjects exposed to benzene (<1 to ≥5 ppm). Second, we used SuperLearner (SL) to identify a minimal number of genes for which altered expression could predict <1 ppm benzene exposure, in 44 subjects with a mean air benzene level of 0.55±0.248 ppm (minimum 0.203ppm). nCounter and microarray expression levels were highly correlated (coefficients >0.7, p<0.05) for 26 microarray-selected genes. nCounter and mRNA-Seq levels were poorly correlated for 4 mRNA-Seq-selected genes. Using negative binomial regression with adjustment for covariates and multiple testing, we confirmed differential expression of 23 microarray-selected genes in the entire benzene-exposed group, and 27 genes in the <1 ppm-exposed subgroup, compared with the control group. Using SL, we identified 3 pairs of genes that could predict <1 ppm benzene exposure with cross-validated AUC estimates >0.9 (p<0.0001) and were not predictive of other exposures (nickel, arsenic, smoking, stress). The predictive gene pairs are PRG2/CLEC5A, NFKBI/CLEC5A, and ACSL1/CLEC5A. They play roles in innate immunity and inflammatory responses. Using nCounter and SL, we validated the altered expression of multiple mRNAs by benzene and identified gene pairs predictive of exposure to benzene at levels below the US occupational standard of 1ppm.

2018-09-06 | GSE119533 | GEO

nCounter analysis of mRNAs associated with GBM tissue using a Nanostring custom assay

Project description:nCounter analysis of mRNAs associated with GBM tissue using a Nanostring custom assay

| PRJNA588829 | ENA

Nanostring nCounter human miRNA assay (v1) of eosinophilic esophagitis

Project description:Nanostring nCounter Human miRNA assay (v1) of esophageal mucosal biopsies from children with eosinophilic esophagitis and controls Individual esophageal mucosal biopsies from children with eosinoniphilic esophagitis and controls were analysed for detection of microRNA

2014-09-01 | E-GEOD-55794 | biostudies-arrayexpress

Nanostring nCounter human miRNA assay (v1) of eosinophilic esophagitis

Project description:Nanostring nCounter Human miRNA assay (v1) of esophageal mucosal biopsies from children with eosinophilic esophagitis and controls

2014-09-01 | GSE55794 | GEO

Custom NanoString Gene Expression Assay for Subtype Identification in Glioblastoma

Project description:Custom NanoString Gene Expression Assay for Subtype Identification in Glioblastoma

| PRJNA737126 | ENA

Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese breast cancer

Project description:Five molecular subtypes have been identified according to intrinsic genes transcription. Microarrays have been adopted for molecular subtyping in addition to the original NanoString nCounter assay. This study aimed to evaluate subtyping consistency among Taiwanese breast cancers. Our study showed that fundamental discrepancy exists between distinct gene expression measuring approaches, and cross platform equivalence should not be overemphasized with too much extrapolation.

2021-09-01 | GSE162228 | GEO

miRQC data for NanoString nCounter miRNA Expression Assays.

Project description:nCounter miRNA Expression Assay data for all profiled miRQC samples prepared by the miRQC Consortium. In this study, we systematically compared 12 commercially available miRNA expression platforms by measuring an identical set of standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression. miRQC Consortium multi-platform comparision. *This represents the NanoString component only

2013-12-30 | E-GEOD-49600 | biostudies-arrayexpress

Gene expression profiling identifies potential biomarkers for colorectal cancer using NanoString nCounter assay

Project description:Gene expression profiling identifies potential biomarkers for colorectal cancer using NanoString nCounter assay

| PRJNA540604 | ENA

nCounter analysis of mRNAs associated with GBM tissue using a Nanostring custom assay

Project description:Gene expression of GBM specimens from untreated and anti-PD-1 treated patients were analyzed using customized 739- gene Nanostring panel

2019-11-12 | GSE140212 | GEO

Nanostring ncounter NHP Immunology V2 panel

Project description:Nanostring ncounter NHP Immunology V2 panel

| PRJNA792145 | ENA