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Expression quantitative trait loci of primary melanocytes facilitate identification of melanoma susceptibility genes

ABSTRACT: eQTL is a powerful method to detect genotype-expression correlation. To be able to identify the genes whose expression levels are correlated with germline genetic variants including the ones associated with melanoma, eQTL analysis was performed in 106 primary melanocyte cultrures

ORGANISM(S): Homo sapiens

PROVIDER: GSE101771 | GEO | 2019/01/01

REPOSITORIES: GEO

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Cell-type specific meQTL extends melanoma GWAS annotation beyond eQTL and identifies a melanocyte gene regulatory network

Project description:To explore the roles of cell-type specific methylation QTL (meQTL) for melanoma GWAS annotation, we generated DNA methylation data from the same sample set as our previouse eQTL study including 106 primary melanocyte cultures. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs in 106 primary melanocyte cultures. To be able to identify the DNA methylation probes whose methylation levels are correlated with germline genetic variants including the ones associated with melanoma, meQTL analysis was performed in these 106 primary melanocyte cultures using the same method as we did for eQTL study.

2021-10-01 | GSE166069 | GEO

NCI Primary Human Melanocyte QTL Study

Project description:<p>In order to create a melanocyte-specific eQTL resource, we obtained primary human melanocyte cultures isolated from foreskin of 106 healthy newborn males predominantly of European descent. Melanocytes were cultured in lot-matched culture medium in randomized batches to minimize variability that could be introduced by culturing conditions. RNA sequencing and direct SNP genotyping of these samples produced an average of ~87.9 million reads (paired-end, stranded, 126bps), and ~713,000 SNP genotypes, respectively.</p>

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Identification of expression quantitative trait loci (eQTL) in human liver

Project description:We performed genome-wide mRNA profiling of 149 human surgical liver samples from Caucasian donors with detailed medical documentation. The overall purpose of the study was to identify expression quantitative trait loci (eQTL) in human liver.

2011-10-10 | GSE32504 | GEO

Identification of expression quantitative trait loci (eQTL) in human liver (SNP)

Project description:We genotyped 149 human surgical liver samples from Caucasian donors with detailed medical documentation. The overall purpose of the study was to identify expression quantitative trait loci (eQTL) in human liver.....

2012-07-03 | GSE39036 | GEO

Genome-wide expression quantitative trait loci (eQTL) analysis in maize

Project description:Background: Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. Results: A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8’-hydroxylase pseudogene.

2011-06-22 | GSE29964 | GEO

Genome-wide expression quantitative trait loci (eQTL) analysis in maize

2011-06-22 | GSE29964 | GEO

Expression quantitative trait loci (eQTL) analysis of Brassica rapa under varying soil phosphorus (P) supplies

Project description:The aim of this study was to identify eQTL in Brassica rapa grown under altered soil phosphorus (P) supply, to understand better the genetic architecture of P-use efficiency (PUE) in plants. Recombinant inbred lines (RILs) of the BraIRRI mapping population were grown at adequate and growth-limiting soil P. Variation in leaf gene expression was quantified using an Agilent Brassica 95k oligonucleotide array. Informative gene expression markers (GEMs) were used to map eQTL and PUE-related QTL. Gene expression was highly dependent on soil P supply. However, the altered expression of many genes, including known P-responsive genes, was highly heritable. Interval mapping using P supply as a covariate revealed 18,876 eQTL, representing 15,912 unique probes. Notable trans-eQTL hotspots occurred on chromosomes A06 and A01; these were enriched with protein modification and phosphorus metabolism-related (A06), as well as chloroplast and photosynthesis-related (A01) transcripts. Regulatory loci and genes associated with P-use efficiency identified through eQTL analysis are potential targets for further characterisation and may have potential for crop improvement. Availability of the annotated B. rapa genome sequence will facilitate their study, including the separation of cis- and trans- effects.

2011-06-29 | GSE27052 | GEO

Expression quantitative trait loci (eQTL) analysis of Brassica rapa under varying soil phosphorus (P) supplies

2011-06-29 | GSE27052 | GEO

Mapping of Hepatic Expression Quantitative Trait Loci (eQTLs) in a Han Chinese Population [Expression analysis]

Project description:Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).

2015-01-02 | GSE53791 | GEO

Mapping of hepatic expression quantitative trait loci (eQTLs) in a Han Chinese population [SNP analysis]

2015-01-02 | GSE53790 | GEO

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