Gallus gallus strain:Broilers
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA247952 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1291160_1.fastq.gz | Fastqsanger.gz | |||
| SRR1291160_2.fastq.gz | Fastqsanger.gz | |||
| SRR1291161_1.fastq.gz | Fastqsanger.gz | |||
| SRR1291161_2.fastq.gz | Fastqsanger.gz | |||
| SRR1291152_1.fastq.gz | Fastqsanger.gz |
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Project description:Gallus gallus cultivar:Broilers Transcriptome or Gene expression
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Project description:Expression of known and predicted genes in tissues of Gallus gallus (chicken) pooled from multiple healthy individuals.
2009-04-16 | GSE12974 | GEO
Project description:We report the transcriptomes of 10 different chicken (Gallus gallus) cell/tissue types. The goal of this project was to determine similarities and differences between different cell/tissue types, with respect to protein coding genes, lncRNA, isoform counts, and differential gene expression. We provide raw data and bigWig files for UCSC visualization. The findings described here will be useful towards a complete annotation of chicken tissue and cellular transcriptomes.
2021-04-26 | GSE166257 | GEO
Project description:The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions. Additionally, general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1) and Cysteine Rich Eggshell Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were proteins known to regulate disulfide cross-linking, suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation. IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg. Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes Keywords: Expression profiling by array
2013-12-01 | GSE52491 | GEO
Project description:Background: High concentrations of atmospheric ammonia are one of the key environmental stressors affecting broiler production performance, which causes remarkable economic losses as well as potential welfare problems of the broiler industry. Previous reports have demonstrated that high levels of ammonia can alter body fat distribution and meat quality of broilers. However, the molecular mechanisms and metabolic pathways in breast muscle altered by high concentrations of ambient ammonia exposure on broilers are still unknown. Results: This study utilized RNA-Seq to compare the transcriptomes of breast muscles to identify differentially enriched genes in broilers exposed to high or low concentrations of atmospheric ammonia. A total of 267 promising candidate genes were identified by differential expression analysis, among which 67 genes were up-regulated and 189 genes were down-regulated. Bioinformatics analysis suggested that the up and down-regulated genes were involved in the following two categories of cellular pathways and metabolisms: Steroid biosynthesis (gga00100) and peroxisome proliferator-activated receptor (PPAR) signaling pathway (gga03320), which both participate in the lipid metabolism processes. Conclusions: This study suggests that longtime exposure to high concentrations of aerial ammonia can change fat content in breast muscle, meat quality and palatability via altering expression levels of genes participating in important lipid metabolism pathways. This study maybe provides new information that could be used for genetic breeding and nutritional intervention in production practice of broilers industry in the future.
2016-07-10 | GSE84099 | GEO
Project description:Gallus gallus gallus strain:lean and fat line Transcriptome or Gene expression
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Project description:Abstract: Atmospheric ammonia is a common problem in poultry industry. High concentrations of aerial ammonia cause great harm to broilers' health and production. For the consideration of human health, the limit exposure concentration of ammonia in houses is set at 25 ppm. Previous reports have shown that 25 ppm is still detrimental to livestock, especially the gastrointestinal tract and respiratory tract, but the negative relationship between ammonia exposure and the tissue of breast muscle of broilers is still unknown. In the present study, 25 ppm ammonia in poultry houses was found to lower slaughter performance and breast yield. Then, high-throughput RNA sequencing was utilized to identify differentially expressed genes in breast muscle of broiler chickens exposed to high (25 ppm) or low (3 ppm) levels of atmospheric ammonia. The transcriptome analysis showed that 163 genes (fold change ≥ 2 or ≤ 0.5; P-value < 0.05) were differentially expressed between Ammonia25 (treatment group) and Ammonia3 (control group), including 96 down-regulated and 67 up-regulated genes. qRT-PCR analysis validated the transcriptomic results of RNA sequencing. Gene Ontology (GO) functional annotation analysis revealed potential genes, processes and pathways with putative involvement in growth and development inhibition of breast muscle in broilers caused by aerial ammonia exposure. This study facilitates understanding of the genetic architecture of the chicken breast muscle transcriptome, and has identified candidate genes for breast muscle response to atmospheric ammonia exposure.
2016-08-19 | GSE85786 | GEO
Project description:Gene expression profile analysis of F2 cross between Fat and Lean chickens
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Project description:Gallus gallus cecal content (broilers in commercial settings) Raw sequence reads
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Project description:The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions. Additionally, general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1) and Cysteine Rich Eggshell Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were proteins known to regulate disulfide cross-linking, suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation. IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg. Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes Keywords: Expression profiling by array A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with AlexaM-BM-. 555 fluorescent dye and the other half with AlexaM-BM-. 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (White isthmus versus magnum and uterus versus white isthmus).
2013-12-01 | E-GEOD-52491 | biostudies-arrayexpress