Comprehensive transcriptional analysis of pig facial skin development
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE231573 | GEO | 2023/05/10
REPOSITORIES: GEO
Similar Datasets
Project description:Comprehensive transcriptional analysis of pig facial skin development
| PRJNA966966 | ENA
Project description:Muscle development and growth is an economically important process in the pig.The neonatal period is another important stage for the pig when the most rapid gain occurring in skeletal muscle.Gene expresseion changes during fetal and postnatal skeletal muscle development that can be used to enhance pig production efficiency, as well as for comparative developmental biology using the pig as a model for other mammalian species. We used microarrays to detail the global programme of gene expression level at different stages of postnatal development. Pig skeletal muscles were selected at different stages of post-natal development for RNA extraction and hybridization on Affymetrix microarrays.So,we sampled at four time-points: within 24 hours after birth (0d),7 days after birth (7d), 14 days after birth (14d), 21 days after birth (21d).
2010-07-07 | E-GEOD-22487 | biostudies-arrayexpress
Project description:Birth Defects: Moebius Syndrome and Related Facial Weakness Disorders
| PRJNA390828 | ENA
Project description:BackgroundSkin development is a complex process that is influenced by many factors. Pig skin is used as an ideal material for xenografts because it is more anatomically and physiologically similar to human skin. It has been shown that the skin development of different pig breeds is different, and some Chinese pig breeds have the characteristics of skin thickness and facial skin folds, but the specific regulatory mechanism of this skin development is not yet clear.MethodsIn this study, the facial skin of Chenghua sows in the four developmental stages of postnatal Day 3 (D3) , Day 90 (D90) , Day 180 (D180), and Year 3 (Y3) were used as experimental materials, and RNA sequencing (RNA-seq) analysis was used to explore the changes in RNA expression in skin development at the four developmental stages, determine the differentially expressed messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), and perform functional analysis of related genes by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.ResultsA pairwise comparison of the four developmental stages identified several differentially expressed genes (DEGs) and found that the number of differentially expressed RNAs (DE RNAs) increased with increasing developmental time intervals. Elastin (ELN) is an important component of the skin. Its content affects the relaxation of the epidermis and dermal connection, and its expression is continuously downregulated during the four developmental stages. The functions of DEGs at different developmental stages were examined by performing GO and KEGG analyses, and the GO terms and enrichment pathways of mRNAs, lncRNAs, miRNAs, and circRNAs highly overlapped, among which the PPAR signaling pathway, a classical pathway for skin development, was enriched by DEGs of D3 vs. D180, D90 vs. D180 and D180 vs. Y3. In addition, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA interaction networks and found genes that may be associated with skin development, but their interactions need further study.ConclusionsWe identified a number of genes associated with skin development, performed functional analyses on some important DEGs and constructed interaction networks that facilitate further studies of skin development.
| S-EPMC10470455 | biostudies-literature
Project description:The pig skin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. To maximize the use of pig skin as a model system to study skin biology, we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pig skin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. In addition, we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.
2021-02-11 | GSE166561 | GEO
Project description:The wide application of pig disease model has caused a surge of interest in the study ofderivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. Our analysis identifies the genes up-regulated in pig iPS compared with somatic cells and also the differentially expressed genes between pig iPSCs under different culture medium. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to M-bM-^@M-^\ribosomeM-bM-^@M-^], M-bM-^@M-^\chromatin remodelingM-bM-^@M-^], and genes involved in M-bM-^@M-^\cell cycle M-bM-^@M-^\that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naM-CM-/ve pluripotency in pig cells.
2015-09-17 | E-MTAB-2634 | biostudies-arrayexpress
Project description:Spermidine-induced recovery of human skin structure and barrier function by skin microbiome
| PRJEB34022 | ENA
Project description:We measured expression profiles of skin fibroblasts harvested during lip cleft surgery of neonates (until 16 days after birth) and children (until 10 years after birth) and compared them to fibroblast isolated from adult skin of breast, scar, and face. We observed clear differences between the cleft and facial fibroblasts and the fibroblasts of breast, as the former originate from the neural crest. Further, we observed differences between adult face fibroblasts and children fibroblasts.
2017-06-11 | E-MTAB-5385 | biostudies-arrayexpress
Project description:The skin is the body's first line of defense and has multiple functions; its development is a complex, multifactorial regulatory process. Porcine skin is physiologically, anatomically and histologically more similar to human skin, and is often used as a model animal for human skin research. There are fewer studies on the transcriptome aspects of the skin during the porcine embryonic period, and the data obtained in this study may help to explain the age-related changes in transcriptional patterns during skin development and provide further reference for understanding human skin development at the molecular level. In this study, RNA sequencing was performed on the dorsal skin of Chenghua sows at embryonic day 56 (E56), embryonic day 76 (E76), embryonic day 105 (E105), and 3 days after birth (D3). Exploring RNA changes in porcine dorsal skin at four ages. Expression profiles of messenger RNAs, long-stranded noncoding RNAs, microRNAs, and cyclic RNAs were analyzed. The biological functions of their differential genes were investigated by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A number of skin-related differential genes were identified by intercomparison between RNAs at four time points, and KEGG functional analysis showed that these differential genes were mainly enriched in metabolic and developmental, immune, and disease pathways,and the pathways enriched in GO analysis were highly overlapping. Collagen is an important part of the skin, with type I collagen making up the largest portion. In this study, collagen, type I, alpha 1 (COL1A1) and collagen typeI alpha2 (COL1A2) was significantly upregulated at four time points. In addition, lncRNA-miRNA-mRNA and miRNA-circRNA co-expression networks were constructed.
2024-02-29 | GSE244092 | GEO