Gallus gallus
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ABSTRACT:
PROVIDER: PRJNA552722 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Restriction-site associated DNA sequencing of Nagoya and White Plymouth Rock meat-type chickens and their F1 and F2 populations
| PRJDB7136 | ENA
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: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
Project description:Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740. The whole blood samples were collected from Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Red Jungle Fowl (RJF), Shouguang (SG), Silkie (SK), Tibetan (TB), Wenchang (WC), and White Plymouth Rock (WR), and genomic DNA was isolated using standard phenol/chloroform extraction methods. Each test sample labeled with Cy3 was mixed with Red Jungle Fowl as reference sample labeled with Cy5. All process and analysis was performed in terms of standard NimbleGen procedure. However, due to some uncontrollable factors, none of results were obtained in three consecutive trials for CS, RIR and WL, so we had to choose a similar Agilent custom-designed 1*1.0 M array.
2015-05-14 | E-GEOD-54117 | biostudies-arrayexpress
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression. Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 14-day-old embryo leg muscle tissues, and the other group consisted of dwarf recessive White Rock 14-day-old embryo leg muscle tissues. The control samples were labeled as A1, A2, A3, and the dwarf chicken samples were labeled as B1, B2, and B3. 9 total embryos per breed, 3 embryos used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system. This submission represents the miRNA profiling component of the study.
2012-04-17 | E-GEOD-37360 | biostudies-arrayexpress
Project description:This submission contains datasets from several species used to demonstrate new features in compareMS2 2.0. Tandem mass spectrometry data from California sea lion, chimpanzee, dog, human, rock hyrax, and white-tailed deer sera were graciously provided with permission from an ongoing collaboration with Dr. Michael G. Janech (College of Charleston) as part of the CoMPARe Program (Comparative Mammalian Proteome Aggregator Resource). Specifically, the California sea lion sera were provided by The Marine Mammal Center (Sausalito, CA), the chimpanzee, rock hyrax, and white-tailed deer sera were provided by The Chattanooga Zoo, and the dog serum from Gus (Ohlandt Veterinary Clinic, Charleston, SC). In addition to institutional and NMFS permits and approval, data collection was performed under NIST ACUC MML-AR20-0001. The identification of certain commercial equipment, instruments, software, or materials does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products identified are necessarily the best available for the purpose.
2022-10-06 | PXD034932 | Pride
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression. Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 7-week-old chicken leg muscle tissues, and the other group consisted of dwarf recessive White Rock 7-week-old chicken leg muscle tissues. The control samples were labeled as A1b, A2b, A3b, and the dwarf chicken samples were labeled as B1b, B2b, and B3b. 9 total chickens per breed, 3 chickens used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system. REPLACE This submission represents the miRNA profiling component of the study.
2012-04-17 | E-GEOD-37367 | biostudies-arrayexpress
Project description:Substantial concentrations of testosterone are not only present in a male's circulation, but also in its ejaculate. Surprisingly, the regulation of ejaculate T and its effects on females and their offspring, potentially a cryptic paternal trait, are not known. We found lower circulating and higher ejaculate T concentrations in subordinate red junglefowl (Gallus gallus gallus) males compared to dominant males, suggestive of an adaptive trade-off in T allocation to circulation and their ejaculate. Subsequently, we artificially inseminated females with either testosterone enriched (TE) or control ejaculates (CE) in a cross-over design. TE females produced heavier eggs than CE females. Offspring growth and tonic immobility were affected in a sex-specific way by TE. TE sons were heavier with shorter TI duration than CE sons, and TE daughters were lighter than CE daughters but daughters did not differ in TI score. However, the chicks competitiveness was not influenced by the TE nor CE. This indicates a previously unknown function of ejaculate testosterone as well as a new form of interaction between a cryptic paternal trait and a maternal effect that may be widespread in the animal kingdom.
| S-EPMC6702165 | biostudies-literature
Project description:Magnum of hen,Egg White and Embryonic Gut 16s rRNA-Seq Raw sequence reads
| PRJNA694626 | ENA