Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from broiler chickens in response to the combined stressors of catching, transport and slaughter

ABSTRACT: The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS. We investigate the differences of gene expression profiles in hepatic tissues between control birds (n=10) and birds experiencing CTS (n=10) using an ARK-Genomics chicken 20K oligo array, a two channel DNA array (http://www.ark-genomics.orgmicroarray) with full dye swap.

ORGANISM(S): Gallus gallus

SUBMITTER: Zhangrui Cheng

PROVIDER: E-GEOD-20953 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from broiler chickens in response to the combined stressors of catching, transport and slaughter

Project description:The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS.

2010-03-19 | GSE20953 | GEO

Transcription profiling of chicken adipose tissue at 7-week of age

Project description:Excessive accumulation of lipids in the adipose tissue is a major problem in the present-day broiler industry. However, few studies have analyzed the expression of adipose tissue genes that are involved in pathways and mechanisms leading to adiposity in chickens. Gene expression profiling of chicken adipose tissue could provide key information about the ontogenesis of fatness and clarify the molecular mechanisms underlying obesity. Chicken Genome Arrays were used to construct an adipose tissue gene expression profile of 7-week-old broilers, and to screen adipose tissue genes that are differentially expressed in lean and fat lines divergently selected over eight generations for high and low abdominal fat weight. Experiment Overall Design: Birds were slaughtered at 7 weeks and abdominal fat was isolated, immediately frozen in liquid nitrogen and stored at -80oC. The ten birds used in the present study were chosen by the percentage of abdominal fat (AFP): five had the highest AFP and the other five had the lowest for RNA extraction and hybridization on Affymetrix microarrays..

2008-11-04 | E-GEOD-8010 | biostudies-arrayexpress

Transcriptome analysis reveals an activation of MHC-I and MHC-II pathways in chicken trachea immunized with infectious laryngotracheitis virus vaccine

Project description:Infectious laryngotracheitis (ILT) is an acute, contagious, upper respiratory disease, which is caused by gallid herpesvirus 1 (GaHV-1). Due to the mortality rates up to 70% depending on the virulence of the virus, it is of economic importance of the disease to explore the etiology of the ILT in the poultry industry. In this study, 15-day-old SPF white leghorn chickens were used to transcriptome analysis in chicken trachea immunized with infectious laryngotracheitis virus vaccine. In conclusion, chicken embryo origin (CEO) vaccine activation of the MHC-I and MHC-II pathways provides insight into the molecular mechanism of immune response in chickens, and holds potential for evaluation and design of new ILT vaccines in a manner adapted to the host immune response to the virus. Ten vaccine inoculated birds were randomly divided in two groups. Each group represents one replication of five pooled tissues, for inoculated birds. Control group consists of five birds that received sterile vaccine diluent.

2014-04-08 | E-GEOD-46046 | biostudies-arrayexpress

Identification of differential duodenal gene expression levels correlated with differences in energy utilization in chickens

Project description:The amount of energy that can be extracted from a diet varies between individuals. Apparent Metabolizable Energy (AME) is a measure of energy utilization efficiency and represents the difference between the energy consumed and the energy lost via the excreta. There are significant differences in the energy utilization capability of individual birds that have a similar genetic background and are raised under identical conditions. We analyzed duodenal gene expression and microbiota differences between birds with different efficiencies in food to energy conversion using microarrays and sequencing of 16s rRNA genes. Differences were found in duodenal gene expression between high and low AME birds, they were however mostly related to genes of unknown function. The flock of 96 chickens was used to study ability of the bird to utilise the energy from feed. We measured energy content in feed and in excreta of individually housed birds. The microarrays were used to compare expression between the best and worst energy utilisers.

2013-06-01 | E-GEOD-47213 | biostudies-arrayexpress

Chicken family BC1 1998: transcriptome profiling used for QTL/eQTL detection

Project description:The family concerns 44 offspring of the sire BC1 n°1998 (produced from a F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al 1980] mated with 8 LL females. Hepatic transcriptomic profiles were obtained using a chicken 20K oligochips (ARK-genomics). The 44 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses

2014-12-22 | GSE16781 | GEO

Chicken family BC1 1940: transcriptome profiling used for QTL/eQTL detection

Project description:The family concerns 46 offspring of the sire BC1 n°1940 (produced from an F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al. 1980]) mated with 8 LL females. Hepatic transcriptomic profiles were obtained using the chicken 20K oligochip (ARK-genomics). The 46 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses.

2008-09-20 | GSE12319 | GEO

Determining the transcriptome of an AdeRS deletion mutant in Acinetobacter baumannii AYE

Project description:RNA sequencing was carried out by ARK genomics, Edinburgh on an Illumina HiSeq platform to compare gene expression in Acinetobacter baumannii strain AYE and an adeRS deletion mutant in this strain.

2016-04-04 | E-MTAB-4047 | biostudies-arrayexpress

Skin transcriptome profiles associated with skin color in chickens

Project description:This work was to study the transcriptome profiles in the skin of chickens with black versus white skin using high-throughput RNA deep-sequencing technology, to investigate the different expression profiles of the genes involved in skin pigmentation, then look for the main differences between black and white skin colors in Lueyang chickens. 16-week-old white and black female Lueyang chickens (5 birds per color) were selected for the sample collection. A piece of skin (8 mm in diameter) from the left back was collected . Total RNA was extracted from the sample using Trizol reagent . Three RNA samples from either the black or white skin samples were pooled following mRNA isolation. The sequencing of the library was performed using an Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China). According the result of sequencing, some colored gene expressions were validated using Real time quantitative polymerase chain reaction (qPCR).

2015-05-20 | E-GEOD-68460 | biostudies-arrayexpress

Infection of chicken with avian influenza H5N1 and H5N2 viruses

Project description:Transcriptional profiling was carried out on lung and ileum samples at 1dpi and 3dpi from chickens infected with either low pathogenic (H5N2) or highly pathogenic (H5N1) avian influenza. Infected birds were compared to control birds at each time point.

2015-01-19 | E-MTAB-2908 | biostudies-arrayexpress

Multiple Arkadia/RNF111 structures coordinate its Polycomb body association and transcriptional control

Project description:The RING domain protein Arkadia/RNF111 is a ubiquitin ligase in the transforming growth factor beta (TGFβ) pathway. We previously identified Arkadia as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD). However, precisely how SUMO interaction contributes to the function of Arkadia was not resolved. Through analytical molecular and cell biology, we found that the SIMs share redundant function with Arkadia's M domain, a region distinguishing Arkadia from its paralogs ARKL1/ARKL2 and the prototypical SUMO-targeted ubiquitin ligase (STUbL) RNF4. The SIMs and M domain together promote both Arkadia's colocalization with CBX4/Pc2, a component of Polycomb bodies, and the activation of a TGFbeta pathway transcription reporter. Transcriptome profiling through RNA sequencing showed that Arkadia can both promote and inhibit gene expression, indicating that Arkadia's activity in transcriptional control may depend on the epigenetic context, defined by Polycomb repressive complexes and DNA methylation [Sun, Liu, and Hunter (2014) Mol Cell Biol 34(16):2981-2995]. To determine the role of Arkadia in TGFβ signaling at the transcriptome level, the profiles of TGFβ-stimulated gene expression were examined in Ark+/+ (Ark_WT), Ark-/- (Ark_null), and Arkadia (WT and sim mutant)-reconstituted Ark-/- MEFs. RNA sequencing was carried out using poly(A)-enriched RNA samples from unstimulated cells and cells treated with TGFβ for 1h, 4h, or 16h as indicated. Two batches of sequencing data for a total of 16 independent samples were submitted.

2015-02-11 | E-GEOD-65796 | 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