Validation of chicken array for gene expression analysis in turkey
Ontology highlight
ABSTRACT:
ORGANISM(S): Meleagris gallopavo Gallus gallus
PROVIDER: GSE66704 | GEO | 2015/03/11
SECONDARY ACCESSION(S): PRJNA277861
REPOSITORIES: GEO
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Project description:Abstract Background: One of the approaches for conducting genomics research in organisms that do not yet have a proper microarray template is to profile their expression patterns by using cross-species hybridization (CSH). Several different studies using spotted microarray for CSH resulted with contradicting conclusions as to the ability of CSH to reflect biological processes. Results: We used a tomato spotted cDNA microarray to examine the ability of CSH to reflect species specific hybridization (SSH) data. Potato RNA was hybridized to spotted cDNA tomato and potato microarrays to generate heterologous and homologous hybridization data, respectively. The results revealed difficulties in obtaining transcriptomics data from CSH that reflected those obtained from SSH. Nevertheless, once the data was filtered for those corresponding to matching probe sets, by restricting proper cutoffs of probe homology, the CSH transcriptomics data better reflected those of the SSH, to an extent that was quantitated by identification of differentially regulated genes. Conclusions: This study enabled us to outline some considerations regarding evaluation of a microarray as candidate platform for CSH study, performance of CSH and proper data analysis that may allow CSH to reflect to some extent a biological process. Keywords: cross-species hybridization; heterologous hybridization
2006-05-30 | GSE3584 | GEO
Project description:The purpose of Experiment 2 was two-fold: a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify differences in gene expression between two genetic lines of turkeys that phenotypically display differences in growth. Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR. Novel candidate genes and pathways were identified as playing potentially crucial roles in skeletal muscle development between 2 distinct lines of turkeys with implications for improving turkey meat quality defects and growth-induced myopathies long-term.
2010-02-01 | GSE19538 | GEO
Project description:The objective of this study was to determine differential gene expression of turkey breast muscle regarding development of PSE meat defect. Genetically unimproved, random-bred (RBC2) turkeys representing turkeys from 1966, which are smaller and grow slower than modern turkeys, were raised at the Michigan State University (MSU) Poultry farm and harvested at 22 week of age. Breast meat was collected and snap frozen in liquid nitrogen. Percent marinade uptake at 24h post-slaughter of each sample was determined. The highest (n=6) and the lowest (n=6) marinade uptake were classified as normal and PSE, respectively. Differentially expressed genes between normal and PSE was identified using TSMLO microarray and confirmed by qRT-PCR. Forty-one oligos were differentially expressed (false discovery rate, FDR<0.1). Candidate genes and pathways associated with development of PSE in turkey were suggested for further experiment to gain greater comprehension about this meat quality defect.
2013-03-20 | GSE36660 | GEO
Project description:The objective of this study was to determine differential gene expression of turkey breast muscle regarding development of PSE meat defect. Genetically unimproved, random-bred (RBC2) turkeys representing turkeys from 1966, which are smaller and grow slower than modern turkeys, were raised at the Michigan State University (MSU) Poultry farm and harvested at 22 week of age. Breast meat was collected and snap frozen in liquid nitrogen. Percent marinade uptake at 24h post-slaughter of each sample was determined. The highest (n=6) and the lowest (n=6) marinade uptake were classified as normal and PSE, respectively. Differentially expressed genes between normal and PSE was identified using TSMLO microarray and confirmed by qRT-PCR. Forty-one oligos were differentially expressed (false discovery rate, FDR<0.1). Candidate genes and pathways associated with development of PSE in turkey were suggested for further experiment to gain greater comprehension about this meat quality defect. Two-condition experiment: normal vs PSE; Biological replicate: n=6 for each condition; Birds were randomly assigned to an array and hybridizations were performed in random order.
2013-03-20 | E-GEOD-36660 | biostudies-arrayexpress
Project description:The male reproductive tract tissue samples were obtained from six 38-wk-old turkeys. The gene expression pattern in turkey testis, epididymis and ductus deferens were determined by high-throughput transcriptome sequencing. The obtained sequence reads were mapped to the turkey genome, and relative expression values were calculated for the analysis of differential expressed genes. Bioinformatics analysis revealed several candidate genes potentially involved in spermatogenesis, spermiogenesis and flagella formation in testis and post-testicular sperm maturation in epididymis and ductus deferens. The achievement of spermatozoa motility during post-testicular maturation were found to be linked with development of flagellum actin filaments and biochemical processes including Ca2+ influx and protein phosphorylation/dephosphorylation. Finally, genes involved in reproductive system development and morphogenesis were identified.
2019-12-21 | GSE142428 | GEO
Project description:The purpose of Experiment 2 was two-fold: a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify differences in gene expression between two genetic lines of turkeys that phenotypically display differences in growth. Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR. Novel candidate genes and pathways were identified as playing potentially crucial roles in skeletal muscle development between 2 distinct lines of turkeys with implications for improving turkey meat quality defects and growth-induced myopathies long-term. This experiment utilized turkeys from two genetic lines: RBC2, a randomly bred control line representative of a 1,967 commercial turkey, and F, a subline genetically selected from the RBC2 line for increased 16-week body weight. Skeletal muscle was collected at three critical developmental stages: 18-day embryo (18de; peak of hyperplasia), 1-day post-hatch (1d; shift from myoblast-mediated growth to satellite cell modulated growth by hypertrophy), and 16-week-old birds (16wk; completion of muscle formation and approximate age of commercial slaughter). Experiment 2 was designed to directly compare the two genetic lines, RBC2 vs. F, for each of the three stages of skeletal muscle development: 18de, 1d, and 16wk. Experiment 2 contained 10 arrays per comparison, therefore, it contained 30 arrays total. Birds were randomly assigned to an array, and hybridizations were performed in random order.
2010-01-31 | E-GEOD-19538 | biostudies-arrayexpress
Project description:Salmonella is one of most common causes of bacterial foodborne disease and consumption of contaminated poultry products, including turkey, is one route of exposure. Minimizing colonization of commercial turkeys with Salmonella could reduce the incidence of Salmonella-associated human foodborne illness. Understanding host responses to these bacteria could lead to potential strategies to minimize colonization and thus food safety risk. In this study, we evaluated bacterial load and blood leukocyte transcriptomic responses of 3-week-old turkeys challenged with the Salmonella enterica serovar Typhimurium (S. Typhimurium) UK1 strain. Turkeys (n = 8/dose) were inoculated with 108 or 1010 colony forming units (CFU) of S. Typhimurium UK1 and fecal shedding and tissue colonization were measured across multiple days post inoculation (dpi). Fecal shedding was 1-2 log10 higher in the 1010 CFU group than the 108 CFU group, but both doses effectively colonized the crop, spleen, ileum, cecum, colon, bursa of Fabricius and cloaca without causing any overt clinical signs in either group of birds. Blood leukocytes were isolated from a subset of the birds (n =3-4/dpi) both pre-infection (0 dpi) and 2 dpi with 1010 CFU and their transcriptomic responses assayed by RNA-sequencing (RNA-seq). After 2 dpi, 647 genes had significant differential expression (DE), including large increases in expression of immune genes such as CCAH221, IL4I1, LYZ, IL13RA2, IL22RA2, and ACOD1. IL1B was predicted as a major regulator of DE in these leukocytes and this DE was predicted to activate cell migration, phagocytosis and proliferation, and to impact the STAT3 and toll-like receptor pathways. These data revealed genes and pathways by which turkey blood leukocytes responded to the pathogen and can provide potential targets for developing intervention strategies or diagnostic assays to mitigate S. Typhimurium in turkeys.
2021-12-31 | GSE151896 | GEO
Project description:Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum Keywords: time course, embryo development
2008-01-31 | GSE9474 | GEO
Project description:Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum Keywords: time course, embryo development
2008-01-31 | GSE9472 | GEO
Project description:Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum Keywords: time course, embryo development
2008-01-31 | GSE9399 | GEO