Broiler Chick Heart RRBS
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39999 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4500970.fastq.gz | Fastqsanger.gz | |||
| ERR4500980.fastq.gz | Fastqsanger.gz | |||
| ERR4500990.fastq.gz | Fastqsanger.gz | |||
| ERR4501000.fastq.gz | Fastqsanger.gz | |||
| ERR4501010.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 87 |
Similar Datasets
Project description:The embryo to neonate transition is a critical period of development that has significant impact on broiler production. During this time important genetic programs governing metabolism and growth are established. The goal of this work was to study the effects of early post-hatch (PH) development and time of initiation of feeding on activation of the genetic programs regulating tissue growth and metabolism in liver, brain, duodenum and breast muscle in broiler chickens. We used chicken genome GeneChip microarrays in a replicated experiment to detail the global program of gene expression in liver, whole brain, duodenum and breast muscle during the post-hatch transition in response to the initiation of feeding. Experiment Overall Design: Tissue samples were collected at hatch and 7 days post-hatch for RNA extraction and hybridization on Affymetrix chicken genome GeneChip microarrays. We analyzed three replicate samples of total RNA on separate microarrays for each tissue at hatch and at day 7 post-hatch in order to increase the resolution of expression profiles. To that end, for each tissue we pooled samples from 4-5 individual chicks at both time points to increase representation of the replicate total RNA samples analyzed on the microarrays.
2009-04-04 | E-GEOD-15413 | biostudies-arrayexpress
Project description:Pre-hatch thermal manipulation of chicks' embryos and post-hatch baicalein supplementation mitigated heat stress in broiler chickens
| PRJNA979953 | ENA
Project description:One-day old white Leghorn chicks were housed in brooders with a 12 hr light:dark cycle, using General Electric chroma 50 fluorescent lighting with irradiance of approximately 50μW/cm2 at chick eye level. They received Purina Chick Chow food and water ad libitum. At one week of age and at the onset of the light phase, the chicks were anesthetized with inhalation ether, and a unilateral translucent white plastic goggle was glued to the periorbital feathers to induce ipsilateral form-deprivation myopia, alternating between the left or right eye. After either 6 hrs (n=8) or 3 days (n=8) of goggle wear, the chicks were killed by decapitation. The enucleated eyes were opened at the equator, and the retina/RPE was dissected together from both the goggled and control eyes. The tissues were individually frozen and stored in liquid nitrogen until processed Keywords: Gene expression
2007-07-26 | GSE6543 | GEO
Project description:The first period post-hatch with all its stimuli could potentially be stressful for the chicks, and by that affect the welfare of the chicken as they mature. By measuring changes in the transcriptome, along with behavioural phenotypes and hormonal levels, the aim is to investigate short and long term effects on the chicken. One batch of chicken were hatched in a production environment, and underwent the same treatment all newly hatched production animals do (sorting, sexing and transportation). Eggs of the same age were simultaneously incubated and hatched in a control environment in a lab. From the end of day one after hatch, both groups were reared under the same conditions in the lab.
2017-02-28 | E-MTAB-4735 | biostudies-arrayexpress
Project description:Aflatoxin is a toxic secondary metabolite produced by the fungi Aspergillus flavus and A. parasiticus. Ingredients of livestock and poultry feed are often contaminated with aflatoxin. Aflatoxin affects many species including humans, dogs, cats, pigs, cattle, and poultry, with liver being the major organ affected. A chicken model was used to evaluate the effect of aflatoxin on hepatic gene expression. Seventy five day-old male broiler chicks were assigned to three dietary treatments (5 replicates of 5 chicks each) from hatch to day 21. The diets contained 0, 1 and 2 mg/kg aflatoxin/kg of feed. Feed intake, body weight gain, liver weights and serum chemistry were evaluated at the end of the study and liver samples were collected in RNase free tubes and stored at -80 ºC. Aflatoxin reduced (P ≤ 0.05) feed intake, body weight, serum total proteins, serum calcium and phosphorus but increased (P < 0.01) liver weights in a dose dependent manner. Microarray experiments were conducted using chicken long oligo arrays, to identify the changes in hepatic gene expression in chicks fed 0 (control) and 2mg/kg aflatoxin/kg of feed. A loop design was followed for microarray experiments with three technical and four biological replicates per treatment group. RNA was extracted from liver tissue and its quality was determined using gel electrophoresis. High quality RNA was purified from DNA contamination, reverse transcribed to cDNA and was used for microarray hybridizations. Microarray data was analyzed using a 2-step ANOVA model using GenePix and MAANOVA softwares, and the differentially expressed genes were identified using SAM, TIGR, and Cluster softwares. The microarray data was validated using real time PCR. It is hypothesized that genes associated with antioxidant, detoxification and immune systems were downregulated and the genes involved in cell proliferation were up-regulated in birds fed aflatoxin compared to controls Keywords: aflatoxin, chicken liver, microarrays, gene expression
2007-07-31 | GSE8603 | GEO
Project description:Abstract Background Chicken embryos emerge from their shell by the piercing movement of the hatching muscle. Although considered a key player during hatching, with activity that imposes a substantial metabolic demand, data are still limited. The study provides a bioenergetic and transcriptomic analyses during the pre-post-hatching period. Methods Weight and morphology alongside content determination of creatine and glycogen were analysed. Transcriptome identified differentially expressed genes and enriched biological processes associated with hatching muscle development, catabolism, and energy provision. Using gene set enrichment, we followed the dynamics of gene-sets involved in energy pathways of oxidative phosphorylation, protein catabolism, glycolysis/gluconeogenesis, and glycogen metabolism. Results Results show several significant findings: (A) Creatine plays a crucial role in the energy metabolism of the hatching muscle, with its concentration remaining stable while glycogen concentration is depleted at hatch and placement. (B) The hatching muscle has the capacity for de-novo creatine synthesis, as indicated by the expression of related genes (AGAT, GAMT). (C) Transcriptome provided insights into genes related to energy pathways under conditions of pre-hatch oxygen and post-hatch glucose limitations (oxidative phosphorylation: NDUF, MT-ND, SDH, UQCR, COX, MT-CO, ATP5, MT-ATP; glycolysis/gluconeogenesis: FBP,G6PC, PFKM; glycogen metabolism: PPP1, PYGL, GYG1). (D) The post-hatch upregulation of protein catabolic processes genes (PSMA, RNF, UBE, FBX), which align with the muscle's weight dynamics, indicates a functional shift from movement during hatching to lifting the head during feeding. Conclusions There is a dynamic metabolic switch in the hatching muscle during embryo-to-hatchling transition. When glycogen concentration depletes, energy supply is maintained by creatine and its de-novo synthesis. Understanding the hatching muscle's energy dynamics is crucial, for reducing hatching failures in endangered avian species, and in domesticated chickens.
2024-11-27 | GSE282902 | GEO
Project description:Early life stage mortality is an important issue for Atlantic cod aquaculture. The impact of the cod maternal (egg) transcriptome on egg quality and mortality during embryonic development is poorly understood. In the present work we studied embryonic mortality and maternal transcript expression using 15 females within an Atlantic cod broodstock development program. Cumulative mortality at 7 days post-fertilization (segmentation stage) and percent hatch were used to assess embryonic survival as an indicator of egg quality. A 20,000 probe (20K) microarray experiment compared the 7 hour post-fertilization (7 hpf, ~ 2-cell stage) egg transcriptome of the two lowest quality females (both with less than 1 percent hatch) to that of the highest quality female (greater than 50 percent hatch).
2014-12-31 | GSE54233 | GEO
Project description:Breast muscle myopathies in broilers compromise meat quality and continue to plague the poultry industry. Broiler breast muscle myopathies are characterized by impaired satellite cells (SC)-mediated repair, and localized tissue hypoxia and dysregulation of oxygen homeostasis have been implicated as contributing factors. The present study was designed to test the hypothesis that hypoxia disrupts the behavior of SC essential for multinucleated myotube formation in vitro, and to determine the extent to which effects are reversed by restoration of oxygen tension. Primary SC was isolated from pectoralis major of young (5 d) Cobb 700 chicks and maintained in growth conditions or induced to differentiate under normoxic (20% O2) or hypoxic (1% O2) conditions for up to 48 h. Hypoxia enhanced SC proliferation while inhibiting myogenic potential, with decreased fusion index and suppressed myotube formation. Reoxygenation after hypoxia partially reversed effects on both proliferation and myogenesis. Western blotting showed that hypoxia diminished myogenin expression, activated AMPK, upregulated proliferation markers, and increased molecular signaling of cellular stress. Hypoxia also promoted accumulation of lipid droplets in myotubes. Targeted RNAseq identified numerous differentially expressed genes across differentiation under hypoxia, including several genes that have been associated with myopathies in vivo. Altogether, these data demonstrate localized hypoxia may influence SC behavior in ways that disrupt muscle repair and promote the formation of myopathies in broilers.
2023-10-24 | GSE241619 | GEO
Project description:Total RNA from in vitro-differentiated murine megakaryocytes incubated for 6hr with 100nM dexamethasone or its vehicle was analyzed using a genome-wide expression microarray using Affymetrix Mouse Transcriptome Array 1.0 arrays.
2023-06-26 | GSE198800 | GEO
Project description:We sequenced mRNA from 34 retina/RPE/choroid samples taken from the right eyes of male chicks across a time-course of normal development or refractive error induction (defocus-induced myopia and hyperopia).
2016-09-17 | GSE78042 | GEO