E-MTAB-6290
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-6290 | ExpressionAtlas | 2019-01-16
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-6290-analysis-methods.tsv | Tabular | |||
| E-MTAB-6290-analytics.tsv | Tabular | |||
| E-MTAB-6290-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-6290-configuration.xml | Xml | |||
| E-MTAB-6290-g1_g2-mvaPlot.png | Other |
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Project description:Down-regulatory responses to heat stress and lipopolysaccharide in the chicken thymic transcriptome
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Project description:For this study, thymic transcriptome responses to an acute heat stress and/or lipopolysaccharide (LPS) were investigated in a broiler line (heat and disease susceptible) and an inbred Fayoumi line (heat and disease resistant) of chickens. In a 2 x 2 design, 22 day-old birds were exposed to heat stress (35°C for 7 hours), lipopolysaccharide (100 µg/kg average body weight per line), or both stressors. Thermoneutral temperature (25°C) and phosphate buffered saline were used as the respective controls. Tissue samples were collected from the thymus and used to isolate high quality RNA. cDNA libraries (n = 31) were constructed and sequenced on the HiSeq 2500.
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Project description:RNA-seq of chicken lines Broiler and Fayoumi bursal transcriptomes in response to heat stress and lipopolysaccharide
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Project description:Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two chicken lines
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Project description:Ethiopia indigenous chicken breeds are typically divided into low and high altitude chicken breeds. Firstly, representative city of low altitude such as Awash is an altitude of around 950 meters above sea level and have a climate which is humidity and high temperature with 37℃ between May and June. Secondly, representative city of high altitude such as Addis Ababa is the capital of Ethiopia in eastern Africa and this city is an altitude of over 2,400 meters above sea level and has a climate which is generally comparable with the average annual temperature of around 16℃. These chicken breeds are adapted to the environmental (climate, temperature and altitude) on the city. Moreover, in Awash, chicken breed is more adapted to heat resistance. So we generated RNA sequencing (RNA-seq) data of Ethiopia indigenous chicken breeds such as low altitude chicken breed (adapted heat) and high altitude chicken breed (Non-adapted heat) to compare the gene expression profiling induced by heat stress (HS). Therefore, we identified 13 hub differentially expressed genes (DEGs) using cuffdiff within cufflinks, which validated by real-time quantitative-PCR (qRT-PCR) in Kenya chicken breed for biological and technical validation. These hub DEGs were subjected to pathway enrichment, protein/protein interaction, and the partial correlation coefficient with information theory (PCIT) to determine their involvement in heat stress and immune response. Our findings suggest that not only hub DEGs but also many others DEGs may play a role in heat stress and immune response.
2018-09-13 | GSE119387 | GEO
Project description:Background: Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression of genes to adapt the cell or organism to survive the heat challenge. RNA-seq technology allows rapid identification of environmentally responsive genes on a large scale. In this study, we have used RNA -seq to identify heat stress responsive genes in the chicken male white-leghorn hepat ocellular (LMH) cell line. Result: The transcripts of 812 genes were responsive to heat stress (p <0.01) with 235 genes up- regulated and 577 down-regulated following 2.5 hours of heat stress. Among the up- regulated were genes whose products function as chaperones, along with genes aff ecting collagen synthesis and deposition, transcription factors, chromatin remodelers and genes modulating the WNT and TGF-beta pathways. Predominant among the down-regulated genes were ones that affect DNA replication and repair along with chromosom al segregation. Many of the genes identified in this study have not been previously implicated in the heat stress response. Conclusion: These data extend our understanding of the transcriptome response to heat stress. Many of the identified biological processes and pathways likely function in adapting cells and organisms to hyperthermic stress. This study may provide important guides to future efforts attempting to improve species abilities to withstand heat stress through genome wide association studies and breeding. In addition, the genes down regulated by heat stress may provide important targets for improving hyperthemic treatment in cancer patients. Cells were grown at either control ( 37oC) or heat stress (43oC) temperatures for 2.5 hours.
2015-02-24 | E-GEOD-55321 | biostudies-arrayexpress
Project description:Background: Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression of genes to adapt the cell or organism to survive the heat challenge. RNA-seq technology allows rapid identification of environmentally responsive genes on a large scale. In this study, we have used RNA -seq to identify heat stress responsive genes in the chicken male white-leghorn hepat ocellular (LMH) cell line. Result: The transcripts of 812 genes were responsive to heat stress (p <0.01) with 235 genes up- regulated and 577 down-regulated following 2.5 hours of heat stress. Among the up- regulated were genes whose products function as chaperones, along with genes aff ecting collagen synthesis and deposition, transcription factors, chromatin remodelers and genes modulating the WNT and TGF-beta pathways. Predominant among the down-regulated genes were ones that affect DNA replication and repair along with chromosom al segregation. Many of the genes identified in this study have not been previously implicated in the heat stress response. Conclusion: These data extend our understanding of the transcriptome response to heat stress. Many of the identified biological processes and pathways likely function in adapting cells and organisms to hyperthermic stress. This study may provide important guides to future efforts attempting to improve species abilities to withstand heat stress through genome wide association studies and breeding. In addition, the genes down regulated by heat stress may provide important targets for improving hyperthemic treatment in cancer patients.
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Project description:We have used RNA-seq to examine mRNAs from chicken spleen and bursa of Fabricius of three different condition (non-immunized and non-heat-stressed (24 ± 1℃ for 3 h), immunized (Newcastle disease vaccine) and non-heat-stressed, and immunized and heat-stressed (36 ± 1℃ for 3 h)). To clarify how chicken immune systems responded to heat stress with and without immunization.
2018-12-01 | GSE93224 | GEO
Project description:By using a 44k chicken Agilent microarray, we systematically analyzed the chicken hypothalamus transcriptome response to thermal stress. Twelve hypothalamus samples were chosen from three groups (four samples per group) to be used in chicken genome microarray to examine differential gene expression.We compared the expression profiles between each pairs of the three groups using the microarray data. Totally, 2474 genes were found to be differentially expressed in the three comparisons with pM-oM-<M-^\0.05 and fold change (FC) higher than 1.5 and the genes were mainly involved in self-regulation and compensation required to maintain homeostasis, including heat shock protein family, enzyme and the hormone, neurotransmitter, cell-cell signaling, metabolism and cytokines. The transcripts of heat shock protein including Hsp 40 and Hsp 90 were significantly changed respond to thermal stress and genes involved in regulation of cell morphogenesis were significantly upregulated in heat stressed group with comparison to control and temperature recovery group. Additionally, the down-regulated genes in both heat stress and temperature recovery groups compared to control group were enriched in muscle organ development, striated muscle tissue development, cardiac muscle tissue development and muscle tissue development, which indicates that muscle development was inhibited during and in short-term after heat treatment. Most of genes dysregulated in heat stress group were found to be recovered in temperature recovery group, which confirmed their roles they could play in coping with heat stress. The present study provides a broader understanding of molecular mechanisms underlying the stress response in chicken and discovery of novel genes that are regulated in a thermal stress specific manner. Hypothalamus samples were collected from non-heat treated group (reared at 25C, used as control), 24h 34C treated group (heat stress treated group) and temperature recovery group (25C for 24h followed heat stress).
2012-10-01 | E-GEOD-37400 | biostudies-arrayexpress
Project description:By using a 44k chicken Agilent microarray, we systematically analyzed the chicken hypothalamus transcriptome response to thermal stress. Twelve hypothalamus samples were chosen from three groups (four samples per group) to be used in chicken genome microarray to examine differential gene expression.We compared the expression profiles between each pairs of the three groups using the microarray data. Totally, 2474 genes were found to be differentially expressed in the three comparisons with p＜0.05 and fold change (FC) higher than 1.5 and the genes were mainly involved in self-regulation and compensation required to maintain homeostasis, including heat shock protein family, enzyme and the hormone, neurotransmitter, cell-cell signaling, metabolism and cytokines. The transcripts of heat shock protein including Hsp 40 and Hsp 90 were significantly changed respond to thermal stress and genes involved in regulation of cell morphogenesis were significantly upregulated in heat stressed group with comparison to control and temperature recovery group. Additionally, the down-regulated genes in both heat stress and temperature recovery groups compared to control group were enriched in muscle organ development, striated muscle tissue development, cardiac muscle tissue development and muscle tissue development, which indicates that muscle development was inhibited during and in short-term after heat treatment. Most of genes dysregulated in heat stress group were found to be recovered in temperature recovery group, which confirmed their roles they could play in coping with heat stress. The present study provides a broader understanding of molecular mechanisms underlying the stress response in chicken and discovery of novel genes that are regulated in a thermal stress specific manner.
2012-10-01 | GSE37400 | GEO