Identification of expression quantitative trait loci (eQTL) in human liver (SNP)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE39036 | GEO | 2012/07/03
SECONDARY ACCESSION(S): PRJNA169674
REPOSITORIES: GEO
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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..... 149 liver samples of Caucasian origin were included in the study on the analysis of RNA expression (Illumina Human_WG6_V2) and genotype (HumanHap_300_V2)
2012-07-02 | E-GEOD-39036 | biostudies-arrayexpress
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
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. 149 liver samples of Caucasian origin were included in the study on the analysis of RNA expression (Illumina Human_WG6_V2) and genotype (HumanHap_300_V1)
2011-10-09 | E-GEOD-32504 | biostudies-arrayexpress
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 | GSE53790 | GEO
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
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
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). Normal (non-diseased) liver tissues were previously collected from 64 Chinese donors who provided informed consent. All samples were stored frozen at -80℃ from collection until processing for RNA and DNA extraction. DNA /Total RNA of the human liver tissue samples were extracted by using the RNA/DNA Mini Kit (Qiagen, Hilden, Germany).each RNA sample were labeled and hybridized to the One-Color Agilent 60-mer Whole Human Genome Microarray (G4112F, GPL4133) at the Agilent Microarray Facility of Shanghai genomePilot Technology, Inc. The genome-wide scan was performed using the Affymetrix Genome-Wide Human SNP Array 6.0. We tested all expression traits for their associations with each of the QC passed SNPs using PLINK's assoc function for quantitative traits, which correlates allele dosage with changes in the trait.
2015-01-02 | E-GEOD-53790 | biostudies-arrayexpress
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. For each of two biological replicates, tissue was collected from B73 and Mo17 parental controls and the IBM2 Syn10 doubled haploid mapping population at 4 weeks after germination (V5 stage). One hundred thirty-five IBM2 Syn10 lines were used in this study. The tissue sampled was the 1.5 cm tip of all crown roots that had developed at the time of harvest, representing the most metabolically active region based on whole-tissue visualization of triphenyl tetrazolium chloride staining. Tissues were flash frozen in liquid nitrogen and stored at -80º C. They were manually ground into a fine powder using a mortar and pestle on dry ice. Two-channel hybridizations were considered as single channel. Therefore, the same raw data file is linked to two Samples appended as _Cy3 and _Cy5.
2011-06-22 | E-GEOD-29964 | biostudies-arrayexpress
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. The experiment was designed to identify expression QTL associated with availability of phosphorus in Brassica rapa. Seventy-eight informative lines from the “BraIRRI” mapping population of Brassica rapa L. (2n = 2x = 10; A-genome) and the two parent lines (IMB211, female; R500, male) were selected for study. The establishment of the BraIRRI population is described by Iniguez-Luy et al. (2009). Plants were grown from seed in compost, under two [P]ext treatments of 9 mg L-1 (low) or 30 mg L-1 (optimal) Olsen extractable P. RNA was extracted from leaf samples from one experimental run (78 lines at low and optimal [P]ext, with one line duplicated i.e. 158 samples), and from leaf samples from the parent lines at low and optimal P in all three experimental runs (12 samples) using a modified TRIzol extraction method (Hammond et al., 2006).
2011-06-29 | E-GEOD-27052 | biostudies-arrayexpress
Project description:To detect genetic variations affecting gene expression in mouse lung tumor tissue, we carried out a genetic linkage study on the transcriptome of lung tumors induced by urethane in an (A/J x C57BL/6)F4 intercross population, whose individual lung tumor multiplicity (Nlung) is linked to the genotype at the pulmonary adenoma susceptibility 1 (Pas1) locus (containing the Kras-37-bp marker) . In particular, susceptible animals carry the A/J-derived version of Pas1 in homozygousity or in heterozygousity, while tumor-resistant animals carry the C57BL/6-derived version. We found that expression levels of 1,179 and 1,579 genes are modulated by an expression quantitative trait locus (eQTL) in cis and in trans, respectively (LOD score > 5). Of note, the genomic area surrounding and including the Pas1 locus regulated 14 genes in cis and 857 genes in trans. In lung tumors of the same (A/J x C57BL/6)F4 mice, we found 1,124 genes whose transcript levels associated with Nlung (FDR < 0.001). The expression levels of about a third of these genes (n = 401) were regulated by the genotype at the Pas1 locus. Pathway analysis of the sets of genes associated with Nlung and regulated by Pas1 revealed a set of 14 recurrently represented genes that are components or targets of the Ras–Erk and Pi3k–Akt signaling pathways. In conclusion, our results illustrate the architecture of germline control of gene expression in mouse lung cancer: they highlight the importance of Pas1 as a tumor-modifier locus, attribute to it a novel role as a major regulator of transcription in lung tumor nodules and strengthen the candidacy of the Kras gene as the effector of this locus.
2016-03-14 | GSE71232 | GEO