RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE57616 | GEO | 2014/05/28
SECONDARY ACCESSION(S): PRJNA247105
REPOSITORIES: GEO
Similar Datasets
Project description:Three-week-old chickens were inoculated with low pathogenic H5N3 AIV and tissues were harvested 4 d pos tinoculation. Four lung cDNA libraries (1 library each for infected and noninfected Leghorn, and infected and noninfected Fayoumi) were prepared and sequenced by Illumina Genome Analyzer II, which yielded a total of 116 million, 75-bp single-end reads.M-BM- The objective of this study was to identify genes and signal pathways associated with resistance to AIV infection in 2 genetically distinct highly inbred chicken lines (Fayoumi, relatively resistant to AIV infection, and Leghorn, susceptible to AIV infection).
2014-05-28 | E-GEOD-57616 | biostudies-arrayexpress
Project description:Avian influenza caused significant damages to the poultry industry, efforts have been made to reveal the disease mechanisms as well as mechanisms of disease resistance. Here, by investigating two chicken breeds with distinct responses to avian influenza virus (AIV), Leghorn GB2 and Fayoumi M43, we compared their differences in genome, methylation and transcriptome. Except for MX1 involved direct acting antiviral mechanism, we found that in both methylation and transcriptome levels the more AIV resistant breed Fayoumi showed less variations compared to White Leghorn after AIV challenging. Fayoumi also showed better consistency between the changes in methylation and changes in transcriptome level. Our results suggested a homeostasis hypothesis of avian influenza resistance, with Fayoumi better maintaining homeostasis both in epigenetic and gene expression levels.
2019-03-15 | GSE128053 | GEO
Project description:To determine the host response to AIV in chicken lungs, a whole chicken genome array was used to analyze RNA isolated from chicken lungs infected with AIV (4dpi) or medium control (NS). Dual-color, direct comparisons were carried between AIV infected and non-infected controls. Each comparison includes four biological replicates. There were 508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. From the results, MX1, IL-8, IRF-7, TNFRS19 are identified as strong candidate genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken.
2012-06-07 | GSE38197 | GEO
Project description:To determine the host response to AIV in chicken lungs, a whole chicken genome array was used to analyze RNA isolated from chicken lungs infected with AIV (4dpi) or medium control (NS). Dual-color, direct comparisons were carried between AIV infected and non-infected controls. Each comparison includes four biological replicates. There were 508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. From the results, MX1, IL-8, IRF-7, TNFRS19 are identified as strong candidate genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken. Dual-color, common reference comparisons were carried between AIV infected and non-infected controls. Four biological replicates, with dye swap labeling, were included in the comparisons. Background subtracted signal intensity were collected from 4 arrays and normalized before data analysis.
2012-06-06 | E-GEOD-38197 | biostudies-arrayexpress
Project description:Domestic chicken has been intensively studied because of its role as an efficient source of lean meat. However, commercial broilers resulting from genetic selection for rapid growth demonstrate detrimental traits, such as excess deposition of abdominal adipose tissue, metabolic disorders, and reduced reproduction. Therefore fast-growing broilers represent “obese” chickens compared to slow-growing egg layers (e.g, Leghorn) or wild strain of meat-type chickens (e.g., Fayoumi). Fayoumi chickens, originating from Egypt, represent a harder stain of chickens, which are more resistant to diseases. Leghorn chickens are the original breed of commercial U.S layers. Both lines were maintained highly inbred by Iowa State University poultry geneticists with an inbreeding coefficient higher than 0.95. Both Fayoumi and Leghorn demonstrated lean phenotype compared to broilers, and these three lines of chickens are genetically distant from each other.
2013-12-23 | GSE44394 | GEO
Project description:Domestic chicken has been intensively studied because of its role as an efficient source of lean meat. However, commercial broilers resulting from genetic selection for rapid growth demonstrate detrimental traits, such as excess deposition of abdominal adipose tissue, metabolic disorders, and reduced reproduction. Therefore fast-growing broilers represent “obese” chickens compared to slow-growing egg layers (e.g, Leghorn) or wild strain of meat-type chickens (e.g., Fayoumi). Fayoumi chickens, originating from Egypt, represent a harder stain of chickens, which are more resistant to diseases. Leghorn chickens are the original breed of commercial U.S layers. Both lines were maintained highly inbred by Iowa State University poultry geneticists with an inbreeding coefficient higher than 0.95. Both Fayoumi and Leghorn demonstrated lean phenotype compared to broilers, and these three lines of chickens are genetically distant from each other. In this study, we used affymetrix microarray to profile global gene expression of three distinct genetic lines of chickens to identify functional pathways associated with leanness of domestic chickens.
2013-12-23 | E-GEOD-44394 | biostudies-arrayexpress
Project description:Background：Dendritic cells (DCs), have the most important antigen presenting ability and played an irreplaceable role in recognizing and clearing virus. Antiviral responses must rapidly defend against infection while minimizing inflammatory damage, but the mechanisms that regulate the magnitude of response within an infected cell are not well understood. MicroRNA, small non-coding RNAs, that can regulate dendritic cells to inhibit the infection and replication of avian influenza virus. Here, we global analyses how avian DCs response to H9N2 avian influenza virus (AIV) and provide a potential mechanism of how avian microRNA defending H9N2 AIV replication. Results： Here, we global analyses how avian DCs response to H9N2 avian influenza virus (AIV) and provide a potential mechanism of how avian microRNA defending H9N2 AIV replication. First, we found that both active and inactive H9N2 AIV enhance the ability of DCs to present antigens and activate T lymphocytes. Next, total microarray analyses suggested that H9N2 AIV stimulation involved in protein localization, nucleotide binding and leukocyte transendothelial migration and MAPK signal pathways. Moreover, we construct 551 transcription factor (TF)-microRNA-mRNA loops based on the above analyses. Furthermore, we found that HA fragment could not activate DCs, while truncated HA highly increased the immune function of DCs by activating ERK and STAT3 signal pathway. Last, our insight research not only gained that gga-miR1644 might target to MBNL2 to enhanced avian DCs in inhibiting virus replication, but also suggested that gga-miR6675 target to the NLS of PB1 to trigger the silencing of PB1 genes and lead to inhibition of H9N2 avian influenza viral replication. All together, our innovative research will shed new light on the roles of avian microRNA in evoking avian DCs and inhibiting virus replication, which will suggest new strategies to combat avian influenza virus.
2017-07-08 | GSE100916 | GEO
Project description:3 genetic chicken lines (Leghorn G-B1, Fayoumi, broiler) were used. chicken were challenged with SE at day 1, spleen and cecum tissues were collected at 2 hours and 16 hours after post challenge Keywords: time-course
2006-04-23 | GSE2562 | GEO
Project description:Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. For this study, Fayoumi, Leghorn, Line A broiler and Line B broiler chicken were chosen. Fayoumi and Leghorn chickens were selected as these two breeds harbor different responses certain pathogens like Avian Influenza Virus and coccidiosis; Broiler Line A and Line B indivduals were chosen as they harbor different intestinal colonization loads to the bacterium Campylobacter jejuni. Campylobacter genetic Line A and genetic Line B are from a commercial producer have been previously described as either resistant (Line A) or susceptible (Line B). Highly inbred chicken lines Fayoumi M15.2 (n=6) and Leghorn GHs6 (n=6) and broilers from Line A (n=24 individuals in pools of 4) and Line B (n=24 individuals in pools of 4)were subjected to array Comparative Genomic Hybridization (aCGH). Each sample was normalized to a Red Jungle Fowl reference. CNVs for each individual and between lines were determined. The major goal of this study was to discover and characterize CNVs in chickens to further narrow in on Quantitative Trait Loci (QTLs) affecting disease response. For the test DNA in Fayoumi and Leghorn, samples from 6 inbred Fayoumi and 6 inbred Leghorn individuals were used; For the test DNA in the Campylobacter genetic lines, samples from 24 individual broilers of Line A (in pools of 4) and 24 individual broilers of Line B (in pools of 4) were used. For the reference DNA, Red Jungle Fowl line UCD001 was used from a self-self hybridization.
2016-02-11 | E-GEOD-44440 | biostudies-arrayexpress
Project description:Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. For this study, Fayoumi, Leghorn, Line A broiler and Line B broiler chicken were chosen. Fayoumi and Leghorn chickens were selected as these two breeds harbor different responses certain pathogens like Avian Influenza Virus and coccidiosis; Broiler Line A and Line B indivduals were chosen as they harbor different intestinal colonization loads to the bacterium Campylobacter jejuni. Campylobacter genetic Line A and genetic Line B are from a commercial producer have been previously described as either resistant (Line A) or susceptible (Line B). Highly inbred chicken lines Fayoumi M15.2 (n=6) and Leghorn GHs6 (n=6) and broilers from Line A (n=24 individuals in pools of 4) and Line B (n=24 individuals in pools of 4)were subjected to array Comparative Genomic Hybridization (aCGH). Each sample was normalized to a Red Jungle Fowl reference. CNVs for each individual and between lines were determined. The major goal of this study was to discover and characterize CNVs in chickens to further narrow in on Quantitative Trait Loci (QTLs) affecting disease response.
2016-02-11 | GSE44440 | GEO