Project description:Chinese indigenous sheep can be classified into two types according to their tail morphology: fat-rumped and thin-tailed sheep, of which the typical breeds are Altay sheep and Tibetan sheep, respectively. To identify the differentially expressed proteins (DEPs) underlying the phenotypic differences between tail types, we used iTRAQ combined with multi-dimensional liquid chromatography tandem mass spectrometry (LC-MS/MS) technology to detect candidate proteins. We then subjected these to a database search, and identified the DEPs. Finally, bioinformatics technology was used to carry out GO functional and KEGG pathway analyses. A total of 3248 proteins were identified, of which 44 were up-regulated and 40 were down-regulated DEPs. Analyzing their GO function terms and KEGG pathways revealed that the functions of these DEPs are mainly binding, catalytic activity, structural molecule activity, molecular function regulator, and transporter activity. Among the genes encoding the DEPs, APOA2, GALK1, ADIPOQ, and NDUFS4 are associated with fat formation and metabolism.
Project description:We identified p63 target genes and binding sites responsible for ectodermal defects by genome-wide profiling of p63 binding using ChIP-seq and expression analysis in human primary keratinocytes from patients with p63 mutations. As proof of principle, we identified a novel de novo microdeletion causing limb defects (SHFM1) that includes a p63 binding site functioning as a cis-regulatory element to control expression of the distally located DLX5/DLX6 genes essential for limb development. Our data demonstrate that target genes and regulatory elements detected in this study can serve as powerful tools to identify causative mutations of unresolved ectodermal disorders. ChIP-seq profiles of p63 in primary human keratinocytes established from two different normal individuals.
Project description:Inherited rickets of Corriedale sheep is characterized by decreased growth rate, thoracic lordosis and angular limb deformities. Previous outcross and backcross studies suggest it is a simple autosomal recessive disorder. A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers. A homozygous region of 199 consecutive single-nucleotide polymorphism (SNP) loci was identified in all the affected sheep, covering a region of 10Mbp on ovine chromosome 6. Among 91 candidate genes in this region, exon 6 of the dentin matrix protein 1 gene (DMP1) was sequenced to reveal 9 SNPs including a nonsense mutation 253T/C which introduced a stop codon (R145X) and could truncate C-terminal amino acids. Genotyping by PCR-RFLP for this mutation showed that, all 17 affected sheep were “T T” genotypes and the 27 phenotypically normal sheep were either “C T” or “C C”. This locus is not in complete linkage disequilibrium with the other 8 SNPs that can all be ruled out as candidates. Previous research has shown that mutations in DMP1 gene are responsible for autosomal recessive hypophosphatemic rickets in humans. Dmp1_knockout mice also exhibit rickets phenotypes. We believe the R145X mutation to be responsible for the inherited rickets found in Corriedale sheep. A simple diagnostic test can be designed to identify carriers with the defective “T” alleles. Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis
Project description:Blood biochemical differences and mechanisms between Bayanbuluk and Turpan black sheep based on multi omics investigation. The digestive tract metabolome, muscle metabolome and lipid metabolome of Bayanbulak sheep, Turpan Black sheep and Altay sheep.
Project description:To explore the coding and non-coding gene expression in the auricular cartilage of microtia patients, we have employed RNA microarray expression profiling as a discovery platform to identify the coding and non-coding genes differentially expressed in microtia patients and controls. The discarded auricular cartilage tissue from 10 unilateral Grade III isolated microtia patients during auricular reconstruction surgery and 5 volunteers without ear malformation or other physical abnormalities during tympanoplasty surgery were collected. All fresh tissues were harvested from the tragus and cavum conchae of the auricle.
2023-07-19 | GSE237360 | GEO
Project description:Altay sheep of gastrointestinal bacteria communities
| PRJNA1094575 | ENA
Project description:Altay sheep of gastrointestinal bacteria communities
Project description:We identified p63 target genes and binding sites responsible for ectodermal defects by genome-wide profiling of p63 binding using ChIP-seq and expression analysis in human primary keratinocytes from patients with p63 mutations. As proof of principle, we identified a novel de novo microdeletion causing limb defects (SHFM1) that includes a p63 binding site functioning as a cis-regulatory element to control expression of the distally located DLX5/DLX6 genes essential for limb development. Our data demonstrate that target genes and regulatory elements detected in this study can serve as powerful tools to identify causative mutations of unresolved ectodermal disorders.
Project description:Inherited rickets of Corriedale sheep is characterized by decreased growth rate, thoracic lordosis and angular limb deformities. Previous outcross and backcross studies suggest it is a simple autosomal recessive disorder. A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers. A homozygous region of 199 consecutive single-nucleotide polymorphism (SNP) loci was identified in all the affected sheep, covering a region of 10Mbp on ovine chromosome 6. Among 91 candidate genes in this region, exon 6 of the dentin matrix protein 1 gene (DMP1) was sequenced to reveal 9 SNPs including a nonsense mutation 253T/C which introduced a stop codon (R145X) and could truncate C-terminal amino acids. Genotyping by PCR-RFLP for this mutation showed that, all 17 affected sheep were “T T” genotypes and the 27 phenotypically normal sheep were either “C T” or “C C”. This locus is not in complete linkage disequilibrium with the other 8 SNPs that can all be ruled out as candidates. Previous research has shown that mutations in DMP1 gene are responsible for autosomal recessive hypophosphatemic rickets in humans. Dmp1_knockout mice also exhibit rickets phenotypes. We believe the R145X mutation to be responsible for the inherited rickets found in Corriedale sheep. A simple diagnostic test can be designed to identify carriers with the defective “T” alleles. Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers to define homozygous regions with consecutive single-nucleotide polymorphism (SNP) loci only existing in all the affected sheep. Fine mapping was conducted by screening coding regions and splicing regions on the positional candidate genes within the homozygous regions by using more sheep