GEO DataSets

(Submitter supplied) 47,880 probe-sets were screened, in the first part of this study, they were analysed for correlation of transcripts levels with body composition traits

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL16569

297 Samples

Download data: CEL

(Submitter supplied) Gene expression data of micro RNA of pig, in the first part of this study, they were analysed for correlation of transcripts levels with body weight and meat quality grade traits

Organism:

synthetic construct; Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

209 Samples

Download data: CEL

(Submitter supplied) In the current work we have compared the transcriptomic and eQTL profiles of the porcine skeletal muscle and liver by using a data set of 103 Duroc pigs genotyped with the Illumina SNP60 BeadChip and with available microarray measurements of gene expression for both tissues.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

206 Samples

Download data: CEL

(Submitter supplied) In this study, we used correlation analysis of the expression profiles and carcass traits to produce a list of functional candidate genes under the assumption that genes with strong correlation between their expression values and drip belong to pathways or networks relevant for the control of the trait. Expression QTL analyses for transcripts showing trait dependent expression were done in order to identify genes which show trait associated expression. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

150 Samples

Download data: CEL

(Submitter supplied) We sequenced mRNA from subcuteneous adipose tissue of 36 pigs (12 Low, 12 Mean and 12 High) to investigate expression profiling of obesity (porcine model). Uploaded RNAseq data on the first 12 samples (from titles 1_SusScrofa to 12_SusScrofa) are LOW obese pigs, the middle 12 samples (from titles 13_SusScrofa to 24_SusScrofa) are MEDIUM obese pigs and the last 12 samples (from titles 24_SusScrofa to 36_SusScrofa) are HIGH obese pigs. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19176

36 Samples

Download data: CSV

(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) Novel, systems-based approach to mouse genetics.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8759

288 Samples

Download data: CEL

(Submitter supplied) In this study, we used correlation analysis of the expression profiles and carcass traits to produce a list of functional candidate genes under the assumption that genes with strong correlation between their expression values and drip belong to pathways or networks relevant for the control of the trait. Expression QTL analyses for transcripts showing trait dependent expression were done in order to identify genes which show trait associated expression.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

207 Samples

Download data: CEL

(Submitter supplied) Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. more...

Organism:

Sus scrofa

Type:

Genome variation profiling by SNP array

Platform:

GPL22170

48 Samples

Download data: CSV, IDAT, TXT, VCF

(Submitter supplied) Boar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19176

96 Samples

Download data: TXT

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

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by SNP array

Platforms:

GPL19176 GPL22170

144 Samples

Download data: IDAT, TXT

(Submitter supplied) Puerto Ricans are a racially admixed population, that consists of European, African and Native American ancestrie. Understanding eQTL patterns in Puerto Ricans should help us elucidate both regulation of gene expression and disease causation in racially admixed populations in general, and in Hispanic subgroups in particular.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

121 Samples

Download data: TXT

(Submitter supplied) Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2,112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters, and enrichment of co-localised functional elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

2112 Samples

Download data: TXT

(Submitter supplied) In order to gain insight into hepatic metabolic pathways and key transcripts affecting traits related to body composition we aimed to compare samples of pigs of two breeds, the “obese” German Landrace (DL) and the “lean” Pietrain (Pi) obtained at prenatal stages (35, 63, and 91 days post conceptionem) and at adult age (180 days). In terms of number of genes regulated the most striking differences between DL and Pi were found at adult age with upregulation of key genes of lipid biosynthesis/metabolism pathways (FASN, ACSS2, ACACA) in obese DL pigs on the one hand and upregulation of genes of cell growth and/or maintenance, protein syntheses as well as cell proliferation pathways (PPARD, POU1F1, IGF2R) in lean Pi pigs on the other hand. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL1881

13 Samples

Download data

(Submitter supplied) Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and transcript abundance. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice shoots at 72 h after germination from 110 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. more...

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

226 Samples

Download data: CEL

(Submitter supplied) A total of 102 garlic accession were performed for mRNA sequencing, and then were used for scoring the variations in both gene sequence (SNPs) and expression (GE) in this population. Thereafter, SNPs and GE are used for carrying out association analysis with the phenotype of shape of garlic clove, respectively, which comes to a joint decision for the candidate genes that are involved in trait. In addition, SNPs and GE data is used as genotype and phenotype, respectively, for performing eQTL analysis to ascertain the interaction among trait-controlled genes, which finally brings a regulatory network for the shape of garlic clove.

Organism:

Allium sativum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23856

102 Samples

Download data: FASTA, XLS

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

206 Samples

Download data: CEL

(Submitter supplied) Pancreatic islet beta cell failure causes type 2 diabetes (T2D). The IMIDIA consortium has used a strategy entailing a stringent comparative transcriptomics analysis of islets isolated enzymatically or by laser microdissection from two large cohorts of non-diabetic (ND) and T2D organ donors (OD) or partially pancreatectomized patients (PPP). This work led to the identification of a signature of genes that were differentially expressed between T2D and ND regardless of the sample type (OD or PPP). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

103 Samples

Download data: CEL, TXT

(Submitter supplied) Pancreatic islet beta cell failure causes type 2 diabetes (T2D). The IMIDIA consortium has used a strategy entailing a stringent comparative transcriptomics analysis of islets isolated enzymatically or by laser microdissection from two large cohorts of non-diabetic (ND) and T2D organ donors (OD) or partially pancreatectomized patients (PPP). This work led to the identification of a signature of genes that were differentially expressed between T2D and ND regardless of the sample type (OD or PPP). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

103 Samples

Download data: CEL, TXT

(Submitter supplied) We applied previously designed array in order to widely cover all types of genes of 74 A. thaliana accessions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL14937

148 Samples

Download data: TXT