Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

55 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Breed gene expression differences in young offspring chicken with Affymetrix Chicken Gene Chip

ABSTRACT: Heritable epigenetic variation in wild and domesticated chickens. Original processed data are available in the archive: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-644/E-MTAB-644.additional.zip

ORGANISM(S): Gallus gallus

SUBMITTER: Daniel Natt

PROVIDER: E-MTAB-644 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transmission of stress-induced learning impairment and associated brain gene expression from parents to offspring in chickens.

Lindqvist Christina C Janczak Andrew M AM Nätt Daniel D Nätt Daniel D Baranowska Izabella I Lindqvist Niclas N Wichman Anette A Lundeberg Joakim J Lindberg Johan J Torjesen Peter A PA Jensen Per P

PloS one 20070411 4

<h4>Background</h4>Stress influences many aspects of animal behaviour and is a major factor driving populations to adapt to changing living conditions, such as during domestication. Stress can affect offspring through non-genetic mechanisms, but recent research indicates that inherited epigenetic modifications of the genome could possibly also be involved.<h4>Methodology/principal findings</h4>Red junglefowl (RJF, ancestors of modern chickens) and domesticated White Leghorn (WL) chickens were ra ...[more]

PMID: 17426812

Publication: 1/6

Similar Datasets

Breed gene expression differences in adult parent chicken with Affymetrix Chicken Gene Chip

Project description:Heritable epigenetic variation in wild and domesticated chickens. Original processed data are available in the archive: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-645/E-MTAB-645.additional.zip

2011-05-10 | E-MTAB-645 | biostudies-arrayexpress

An atlas of mRNA expression in pig adipose and muscle tissues

Project description:Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism. The mRNA expression differences of eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates are measured.

2012-05-15 | E-GEOD-30343 | biostudies-arrayexpress

Proteomic analysis of protein profile of blood serum of patients with autism children

Project description:A comparative panoramic mass spectrometric analysis of serum samples from three families with children with autistic disorders was carried out. The total number of examined samples was nine, including four control samples from healthy parents, and five samples from autistic children.

2016-11-01 | PXD005193 | Pride

Maternal western diet primes susceptibility to hepatic inflamation in adult male mouse offspring

Project description:Background & Aims: The influences of the maternal diet during gestation has been suggested to be involved in the development of different aspects of the metabolic syndrome. In our mouse model we characterised the role of maternal western diet in the development of non-alcoholic fatty liver disease (NAFLD) in the offspring. Methods: Female mice were fed either a western (W) or low-fat control (L) semi-synthetic diet before and during gestation and lactation. At weaning, male offspring were assigned either the W or the L diet, generating four experimental groups: WW, WL, LW and LL offspring. Biochemical, histological and epigenetic indicators were investigated at 29 weeks of age. Results: Male offspring exposed to prenatal western style diet and to a post-weaning W diet (WW) showed hepatomegaly combined with increased hepatic cholesterol and triglycerides accumulation, compared to LW offspring. This was associated with up-regulation of de novo lipid synthesis and dysregulation of beta oxidation and lipid storage. Elevated hepatic transaminases and increased expression of Tnfa, Cd11, Mcp1 and Tgfb underpin the severity of liver injury. Histological analysis supported the presence of steatohepatitis in the WW offspring. In addition alterations in DNA methylation in key metabolic genes (Ppara, Insig, Fasn) were detected. Conclusion: Maternal dietary fat intake during critical developmental phases programs susceptibility to liver disease in mouse offspring. This was mediated by shifts in lipid metabolism and inflammatory response. Long lasting epigenetic changes may underlie this dysregulation 4 groups of 6 male mouse were analysed , 1 experimental and 1 biological outlier was excluded , so n=6,5,5,6 in the 4 groups (LL,LW,WL,WW)

2014-01-21 | E-GEOD-44901 | biostudies-arrayexpress

An atlas of DNA methylomes in pig adipose and muscle tissues

Project description:It is evident that epigenetic factors, especially DNA methylation, play essential roles in obesity development. To learn systematic association of DNA methylation to obesity, we used pig as a model, and sampled eight diverse adipose tissues and two distinct skeletal muscle tissues from three pig breeds with distinguished fat levels: the lean Landrace, the fatty Rongchang, and the feral Tibetan pig. We sequenced 180 methylated DNA immunoprecipitation (MeDIP) libraries, generated 1,381 Gbp sequence data, and provided a genome-wide DNA methylation map for pig adipose and muscle studies. The analysis showed global similarities and differences between breeds, genders and tissues, and identified the differentially methylated regions (DMRs) that are preferentially located in intermediate CpG promoters and CpG island shores. The DMRs in promoters are highly associated to obesity development. We also analyzed methylation and regulation of the known obesity-related genes and predicted novel candidate genes. The comprehensive map here provides a solid base for exploring epigenetic mechanisms of adipose deposition and muscle growth. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied genome-wide DNA methylation differences among breeds, males and females, and tissues.

2012-05-16 | E-GEOD-30344 | biostudies-arrayexpress

Transcriptomics response to miR-644 overexpression in three breast cancer cell lines

Project description:The goal of the study is to investigate the effect of microRNA-644 overexpression by chemical mimics on gene expression in breast cancer cell lines. To this purpose control and microRNA-644 mimics are used to transfect MDA-MB-231 cells, SK-BR-3 cells, and MCF-7 cells respectively. Transcriptomics profiling was performed with Illumina HumanHT-12 V4.0 BeadChip microarray. Three cell lines are treated with scramble microRNA mimic (control herein) and microRNA-644 mimic (miR-644 herein), with two replicates per condition. mRNA expression is compared between miR-644 and control treatment within each cell line, respectively.

2016-07-25 | E-GEOD-82058 | biostudies-arrayexpress

Genome-wide DNA methylation profiling reveals epigenetic changes in the rat nucleus accumbens associated with cross-generational effects of adolescent THC exposure

Project description:Drug exposure during critical periods of development is known to have lasting effects, increasing one’s risk for developing mental health disorders. Emerging evidence has also indicated the possibility for drug exposure to even impact subsequent generations. Our previous work demonstrated that adolescent exposure to Δ9-tetrahydrocannabinol (THC), the main psychoactive component of marijuana (Cannabis sativa), in a Long-Evans rat model affects reward-related behavior and gene regulation in the subsequent (F1) generation unexposed to the drug. Questions, however, remained regarding potential epigenetic consequences. In the current study, using the same rat model, we employed Enhanced Reduced Representation Bisulfite Sequencing to interrogate the epigenome of the nucleus accumbens, a key brain area involved in reward processing. This analysis compared 16 animals with parental-THC exposure and 16 without to characterize relevant systems-level changes in DNA methylation. We identified 1,027 differentially methylated regions (DMRs) associated with parental THC exposure in F1 adults, each represented by multiple CpGs. These DMRs fell predominantly within introns, exons, and intergenic intervals, while showing a significant depletion in gene promoters. From these, we identified a network of DMR-associated genes involved in glutamatergic synaptic regulation, which also exhibited altered mRNA expression in the nucleus accumbens. These data provide novel insight into drug-related cross-generational epigenetic effects, and serve as a useful resource for investigators to explore novel neurobiological systems underlying drug abuse vulnerability. Study consisted of a total of 32 F1 individuals (Long-Evan rats); 16 animals (8 female, 8 male) were offspring from THC-exposed parents, and the remaining 16 animals (8 female, 8 male) were offspring from saline-exposed parents ("controls"; "VEH-exposed").

2015-06-19 | E-GEOD-69984 | biostudies-arrayexpress

Genome-wide copy number variation in Chinese schizophrenia trios

Project description:To reveal the risk CNVs of SZ in Chinese population, we recrited and enrolled 100 Chinese family trios with a schizophrenia affected children and both of their father and mother. SZ was diagnosed according to DSM-IV criteria by two independent psychiatrists. There gDNA we screen the genome-wide CNV using Agilent SurePrint G3 Human CGH Microarray Kit (1x1M) and Agilent sex-matched human DNA was used as reference. The CNV were called by ADM-2 statistical algorithms with a threshold of 6.0. We compared the burden of large rare CNVs and found that SZ probands carried more duplications and less deletions. Furtherly, we performed familial inheritance analysis of transmission disequilibrium and de novo CNV detection, validated several associated CNV loci with SZ susceptibility and also identify eight novel loci conferring risk of SZ

2021-10-01 | E-MTAB-8075 | biostudies-arrayexpress

Transcriptomics response to miR-644 overexpression in three breast cancer cell lines

2016-07-25 | GSE82058 | GEO

Transgenerational early stress affymetrix gene expression male offspring chicken

Project description:Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The data for the parental stressed and control birds is available in ArrayExpress with accession E-MTAB-924, while this experiment only concerns their offspring that never been exposed to early life stress.

2012-01-02 | E-MTAB-925 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data