GEO DataSets

(Submitter supplied) eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions

Organism:

Arabidopsis thaliana

Type:

Expression profiling by SNP array; Expression profiling by genome tiling array

Platform:

GPL10855

57 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; Expression profiling by genome tiling array; Expression profiling by SNP array

Platform:

GPL8655

43 Samples

Download data: CEL

(Submitter supplied) Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regulatory effect was identified as allele specific expression in F1 hybrids. Composite trans regulatory effect was detected as deviation between parental expression and F1 hybrids expression.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array; Expression profiling by SNP array

Platform:

GPL8655

12 Samples

Download data: CEL

(Submitter supplied) Genomic DNA of Col-0 and Van-0 were mixed at 1:1 and labeled using Bioprime randon labeling kit. A total of 16ug labelled products were hybridized to AtSNPtile1. Used as the reference of equal allele expression.

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

Platform:

GPL8655

4 Samples

Download data: CEL

(Submitter supplied) Genomic DNA of Col-0, Van-0 and their mixture at different proportion were labeled using Bioprime randon labeling kit. A total of 16ug labelled products were hybridized to AtSNPtile1. This experiment is to test whether the log allele intensity ratio efficiently detects the allelic variation within targets.

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

Platform:

GPL8655

17 Samples

Download data: CEL

(Submitter supplied) Genomic DNA of COl-0 and Van-0 were labeled using Bioprime randon labeling kit. Labelled products were hybridized to AtSNPtile1 at a total amount of 6ug, 9ug, 12ug, 15ug, and 18ug. This experiment is to test whether the overall target amount affect the log allele intensity ratio.

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

Platform:

GPL8655

10 Samples

Download data: CEL

(Submitter supplied) The identification of multiple signals at individual loci could explain additional phenotypic variance ('missing heritability') of common traits, and help identify causal genes. We examined gene expression levels as a model trait because of the large number of strong genetic effects acting in cis. Using expression profiles from 613 individuals, we performed genome-wide single nucleotide polymorphism (SNP) analyses to identify cis-expression quantitative trait loci (eQTLs), and conditional analysis to identify second signals. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

705 Samples

Download data: TXT

(Submitter supplied) Efforts to improve resilience in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL19893

243 Samples

Download data: TXT

(Submitter supplied) We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).

Organism:

Arabidopsis thaliana x Arabidopsis lyrata; Arabidopsis thaliana; Arabidopsis lyrata

Type:

Expression profiling by SNP array; Genome variation profiling by SNP array

Platform:

GPL13483

24 Samples

Download data: CEL

(Submitter supplied) This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse A. thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along the A. thaliana genome with ~35 bp resolution. The reference genome for the array design is Columbia-0. more...

Organism:

Arabidopsis thaliana

5 Series

71 Samples

Download data: CDF, TXT

(Submitter supplied) Understanding the patterns and processes driving natural genetic variation in gene expression is of fundamental importance to biology. In this study, we examined genetic variation in gene transcription through expression QTL (eQTL) analysis in the Tsu-1 x Kas-1 recombinant inbred line (RIL) mapping population of Arabidopsis thaliana. To understand how natural variation in transcription responds to abiotic stress, we conducted eQTL in both well watered and soil drying conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL16303

208 Samples

Download data: CEL

(Submitter supplied) Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5 – 2 μg Cd g-1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. more...

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by SNP array; Genome variation profiling by genome tiling array

Platform:

GPL10855

2 Samples

Download data: CEL, TXT

(Submitter supplied) We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. more...

Organism:

Arabidopsis thaliana x Arabidopsis lyrata; Arabidopsis thaliana x Arabidopsis halleri

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21749 GPL21748

18 Samples

Download data: TXT

(Submitter supplied) Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

42 Samples

Download data: CEL, TXT

(Submitter supplied) We applied a massively parallel reporter assay (MPRA) in lymphoblastoid cells to functionally evaluate 49,256 allelic pairs, representing 30,893 genetic variants in high, local linkage disequilibrium for 744 independent cis-expression quantitative trait loci (eQTLs) assessed for colocalization across 114 traits.

Organism:

Homo sapiens; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26526 GPL24676

7 Samples

Download data: TXT

(Submitter supplied) The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and a wide range of BP-related quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

786 Samples

Download data: TXT

(Submitter supplied) Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. more...

Organism:

Arabidopsis suecica; Arabidopsis arenosa x Arabidopsis thaliana; Arabidopsis thaliana; Arabidopsis arenosa

Type:

Expression profiling by high throughput sequencing

4 related Platforms

5 Samples

Download data: TXT

(Submitter supplied) We developed a method that perturbs transcription factor followed by monitoring genome-wide allelic expression measurements in living cells. As a model for this novel approach, we chose the factor NFκB.

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array; Genome variation profiling by genome tiling array

Platform:

GPL14157

27 Samples

Download data: IDAT

(Submitter supplied) This set of data was used to identify cis-regulatory SNPs by measuring allelic gene expression. From analyzing cis-regulatory SNPs from different tissues, cis-regulatory SNPs common across tissues or the cell-type specific were cataloged.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL6983 GPL6984

219 Samples

Download data: TXT

(Submitter supplied) Most variants associated to diseases are located in non-coding regions of the genome, and are thought to be regulatory in nature. Cis-regulatory SNPs (cis-rSNPs) impacting transcription can be identified through the mapping of differences in allelic expression (AE). We mapped common cis-rSNPs of protein coding and non-coding genes in 3 distinct cell-types. We show 70% sharing across tissues and similar genetically controlled transcription for protein-coding genes and lincRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL9115

41 Samples

Download data: BED, FPKM_TRACKING