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: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: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: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:Spermidine-induced recovery of human skin structure and barrier function by skin microbiome
| PRJEB34022 | ENA
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
Project description:In this study, miRNA-seq technique was used to identify differentially expressed miRNAs (DE miRNAs) in cardiac muscle of the Tibetan pig (TP) and Yorkshire pig (YP), which were both raised in highland environments. We obtained 108 M clean reads and 372 unique miRNAs that included 210 known pre-miRNAs and 162 novel pre-miRNAs. In addition, 20 DE miRNAs, including 10 upregulated and 10 downregulated miRNAs, were identified by comparing TP and YP. Based on the expression abundance and differentiation between the two populations, we predicted their targets, and KEGG pathway analyses suggested that DE miRNAs between the Tibetan pigs and Yorkshire pigs are involved in hypoxia-related pathways, such as the MAPK, mTOR, and VEGF signaling pathways, cancer-related signaling pathways, etc. Five DE miRNAs were randomly selected to validate the veracity of miRNA-seq using real-time PCR. The results showed that the expression corresponds to the trend in miRNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related miRNAs in pig and indicated that the expression patterns of hypoxia-related miRNAs are significantly altered in the Tibetan pig. DE miRNAs may play important roles in hypoxic adaptation after migration to hypoxic environments. mRNA profiles of 6-month old Tibetan pig (TP) and Yorkshire pig (YP) were generated by deep sequencing, in duplicate, using Hiseq 2000.
2015-07-31 | E-GEOD-71550 | biostudies-arrayexpress
Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context. Eleven small RNA libraries from eight adipose tissues, two skeletal muscle tissues and cardiac muscle of pig were sequenced.
2012-05-16 | E-GEOD-30334 | biostudies-arrayexpress
Project description:We performed carefully designed and controlled animal feeding studies. We devided 9 adult rats in three group and each group fed with one type of diets in 28 days: rice, potatoes and chow. We fed piglets in triplicate either with cow milk or let them feed from sows milk for 4 weeks followed by 7 weeks of maize diet. Based on the small RNA sequencing data from 9 rat and 6 pig serum samples, we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood.
2017-01-01 | GSE92897 | GEO