E-MTAB-6289
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-6289 | ExpressionAtlas | 2019-01-16
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-6289-analysis-methods.tsv | Tabular | |||
| E-MTAB-6289-analytics.tsv | Tabular | |||
| E-MTAB-6289-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-6289-configuration.xml | Xml | |||
| E-MTAB-6289-g1_g2-mvaPlot.png | Other |
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Project description:RNA-seq of response to heat stress and lipopolysaccharide in the thymic transcriptome of chicken broiler and fayoumi lines
2019-01-16 | E-MTAB-6290 | ExpressionAtlas
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.
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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:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
2020-02-14 | MTBLS1320 | MetaboLights
Project description:Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two chicken lines
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Project description:To realize the gene expression in response to acute heat stress in chicken testis, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Male B strain Taiwan country chickens were subjected to acute heat stress (38M-bM-^DM-^C) for 4 h, and then exposed to 25M-bM-^DM-^C, with testes collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed roosters as a control group (n = 3 roosters per group). Based on a chicken 44K oligo microarray, 163 genes significantly differed in the testes of the heat-stressed chickens from those of the control chickens. The mRNA expressions of upregulated genes, including HSP25, HSP90AA1, HSPA2, and LPAR2, and downregulated genes, including CDH5, CTNNA3, EHF, CIRBP, SLA, and NTF3, were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR). Acute heat stress induced testicular gene experssion in B strain Taiwan country chicken was measured at 0, 2, and 6 h of recovery after 4 h of 38 degree acute heat stress.
2015-01-27 | E-GEOD-65279 | 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. 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:To realize the gene expression in response to acute heat stress in chicken testis, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Male B strain Taiwan country chickens were subjected to acute heat stress (38℃) for 4 h, and then exposed to 25℃, with testes collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed roosters as a control group (n = 3 roosters per group). Based on a chicken 44K oligo microarray, 163 genes significantly differed in the testes of the heat-stressed chickens from those of the control chickens. The mRNA expressions of upregulated genes, including HSP25, HSP90AA1, HSPA2, and LPAR2, and downregulated genes, including CDH5, CTNNA3, EHF, CIRBP, SLA, and NTF3, were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).
2015-01-27 | GSE65279 | 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.
2015-02-24 | GSE55321 | 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