Transcriptomes From the Deep Cones During FIbroproliferative Cutaneous Healing in the Duroc/Yorkshire Porcine Model
ABSTRACT: The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time. Overall design: We made shallow and deep wounds on the backs of 3 Yorkshire and 3 Duroc pigs, biopsied the wounds at 1 2 3 12 and 20 weeks, extracted and amplified the RNA from the deep cones, and hybridized the Affymetrix GeneChip®. We compared wound depth by breed over time; the system included 3 factors (depth, breed and time). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
INSTRUMENT(S): [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Project description:The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time. We made shallow and deep wounds on the backs of 3 Yorkshire and 3 Duroc pigs, biopsied the wounds at 1 2 3 12 and 20 weeks, extracted and amplified the RNA from the deep cones, and hybridized the Affymetrix GeneChip®. We compared wound depth by breed over time; the system included 3 factors (depth, breed and time). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
Project description:The goal was to obtain the differential transcriptome in the deep cones fibroblasts between shallow and deep wounds in Duroc breeds at 20 wks. We made shallow and deep wounds on the backs 2 Duroc pigs, biopsied the wounds at 20 weeks, cultured fibroblasts, extracted and the RNA from the cultured fibroblasts, and hybridized the Affymetrix GeneChip. We compared wound depth, the system included 1 factors (depth). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
Project description:In this study, RNA-seq technique was used to identify differentially expressed genes (DEGs) in cardiac muscle of the Tibetan pigs raised at highland (TH), Tibetan pigs raised at lowland (TL), Yorkshire pigs raised at highland (YH) and Yorkshire raised at lowland (YL). We obtained 551M clean reads and detected 18585 genes that were expressed in the eight heart samples. According to a standard of fold-change (FC>2 or FC <0.5) and difference significant (P<0.05), obtained 299, 169, 242 and 368 of significantly differentially expressed genes (DEGs) respectively in TH vs.YH, TH vs.TL, TL vs.YL and YH vs.YL. GO and pathways analysis for DEGs results showed enrichment in HIF-1 signaling pathway, and hypertrophic cardiomyopathy (Hypertrophic cardiomyopathy (HCM), cardiovascular development, immunity, DNA damage and other biological functions. Eight DEGs were randomly selected to validate the veracity of RNA-seq and using real-time PCR. The results showed that the expression corresponds to the trend in RNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related genes in pig and indicated that the expression patterns of hypoxia-related genes are significantly altered in the Tibetan pig. DEGs may play important roles in hypoxic adaptation after migration to hypoxic environments. Overall design: mRNA profiles of 6-month old Tibetan pigs raised at highland (TH), Tibetan pigs raised at lowland (TL), Yorkshire pigs raised at highland (YH) and Yorkshire raised at lowland (YL) were generated by deep sequencing, every pig breed has two replicates, using Hiseq 2000.
Project description:Intramuscular fat (IMF) content is an important trait closely correlated with meat quality, which is highly variable among swine breeds from diverse genetic backgrounds. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA-sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. A total of 717 differentially expressed genes (DEGs) were identified in our study, with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. GO analysis showed that DEGs significantly related to muscle proliferation and development, lipid storage and catabolic, extracellular matrix structural constituent, and neutral amino acid transmembrane transporter activity. Pathway analysis revealed that DEGs associated with fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, protein digestion and absorption, and amino acid metabolism. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs from both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes for affecting pork quality. Overall design: Transcriptome sequencing in longissimus dorsi muscle of Wei and Yorkshire pigs
Project description:Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, respiratory symptoms in piglets, and high mortality. In this study, we employed Affymetrix microarray chip technology to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited the range of clinical features that typify the disease, while the DPL pigs exhibited only mild signs of the disease. The percentage of CD8+ T cells in the DPL pigs was significantly higher than that in the DLY pigs at 21 days post-infection (dpi) (p< 0.05). Interleukin (IL) 1 beta (IL-1β) and IL-2 levels showed significant differences between the DPL and DLY pigs at 0 and 7 dpi (p< 0.01). For IL-10, the DLY pigs had significantly higher values than the DPL pigs at 0 and 7 dpi (p< 0.01). Significant differences were apparent between the DPL and DLY pigs in terms of their tumor necrosis factor-alpha (TNF-α) and interferon (IFN)-gamma (IFN-γ) levels at 0 and 7 dpi (p< 0.01). Microarray data revealed 16 differentially expressed genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The expression levels of 10 of the 16 genes, namely CCDC84, C6ORF52, THYMOSIN, PRVE, HSPCB, CYP2J2, AMPD3, TOR1AIP2, PTGES3, and ACOX3, were validated by real-time quantitative RT-PCR. This study provides a platform for further investigation of the molecular mechanisms underlying the differential immune responses to PRRSV infection in different breeds or lines of pig. We investigated the response of lung tissues from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs infected with porcine reproductive and respiratory syndrome virus (strain JXA1) by using the Affymetrix Porcine Genome Array. Sixteen healthy 30-day-old weaned DPL pigs were selected from the Jiaxiang Dapulian farm, Jining City, China, and 15 healthy 30-day-old weaned DLY pigs were obtained from a commercial farm with high standards of animal health. These pigs were free from PRRSV, porcine circovirus type 2 (PCV2), pseudorabies virus (PRV), and classical swine fever virus (CSFV) as determined by ELISA tests for serum antibodies; the absence of PRRSV was also confirmed by real-time quantitative reverse transcription PCR (qRT-PCR). Pigs were randomly assigned into two groups and reared in separate places: the PRRSV-infected group consisted of 11 DPL and 10 DLY pigs, and the control group consisted of five DPL and five DLY pigs. Infections in the pigs proceeded via inoculation with 2 ml of a viral suspension of PRRSV (at a tissue culture infectious dose of 105) by dripping the solution into the nasal cavity of each pig. The control group was treated with an identical volume of PBS by the same method. Rectal temperatures and clinical examinations on the pigs were recorded daily during the experiment. Anticoagulant-treated blood and untreated blood samples were collected separately at 0, 7, 14, and 21 days post-infection (dpi) from the infected and control groups for assaying CD4+, CD8+, cytokine (interleukin (IL) 1 beta (IL-1β), IL-2, IL-10, interferon (IFN)-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and immunoglobulin G (IgG) protein levels. Lung samples for microarray analysis and real-time qRT-PCR analysis were collected from six infected DLY and DPL pigs (three pigs for each breed) immediately post-slaughter at 28 dpi. Total RNA was isolated from lung tissue samples and purified using an RNeasy Mini kit according to the manufacturer’s protocol. RNA was prepared using the GeneChip (AFF-900623) one cycle target for the labeling and control reagents, and the labeled RNA was hybridized in an Affymetrix Hybridization Oven 640 for sequencing.
Project description:Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by pre-slaughter stress or no stress treatment in pigs of different breed (Italian Duroc, Italian Large White or Pietrain) and differnt Halothane genotype (RYR1 locus CC-NN, CT-Nn or TT-nn) in Pietrain pigs. All 36 samples were hybridised together with a common reference.
Project description:Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by pre-slaughter stress or no stress treatment in pigs of different breed (Italian Duroc, Italian Large White or Pietrain) and differnt Halothane genotype (RYR1 locus CC-NN, CT-Nn or TT-nn) in Pietrain pigs. Overall design: All 36 samples were hybridised together with a common reference.
Project description:The starch, acting as the major energy-producing component of the daily diet, is the main carbohydrate in mammal nutrition. However, the nutritional value of starch can vary widely depending upon its source and site of digestion. The distinct physiological responses were previously observed both in human and other mammals, but still little is known about the underlying mechanisms regarding the metabolic shifts due to the intake of various dietary starches. Here, we assessed the overall metabolic changes in weaned pigs induced by different dietary starch sources at the transcriptome level. Sixteen weaned pigs (Duroc×Landrace×Yorkshire) were selected and randomly allotted to diets containing either wheat (WH) or cassava (CA) starch as the energy source (n=8). We measured serum metabolites and hormones and generated transcriptional profiles of liver. 648 genes in liver were differentially expressed in response to dietary starch sources. Pathway analysis indicated that dietary starch sources altered both carbohydrate and lipid metabolism in liver. In contrast, CA may be more healthful as dietary energy source than WH by down-regulating lipogenesis and steroidogenesis in liver. Sixteen weaned pigs (Duroc×Landrace×Yorkshire) with an average initial body weight of 7.37±0.25 kg were selected and randomly allotted to two dietary treatments (either wheat or cassava starch as the energy source) for 21 d. At the end of the trial, the liver tissue were collected for transcriptome analysis using Agilent porcine microarrays.
Project description:Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material. Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes. Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development. Overall design: Sixteen animals, four from each of four breeds, Large White (LW), Duroc (DU), Youli (YL) and Iberian (IB) piglets were sampled. These breeds represent a wide genetic variability in current pig breeding schemes. There were two males and two females per breed except in Youli, represented by three males and one female. Animals were bought from three breeding companies and transferred to the University experimental farms at weaning, i.e., aged one month approximately. Pigs were housed simultaneously, fed the same diets during the fattening period, that lasted two months, and were weighed at weekly intervals. At the time of slaughter, the average ages were 87, 83, 80 and 89 days for Large White, Duroc, Youli and Iberian pigs, respectively. Their mean live weights at that time were 27.2 (LW), 23.1 (DU), 18.9 (YL) and 17.4 kg (IB). Animals were euthanized, after 24h fasting, by an overdose of intravenous sodium thiobarbital. At necropsy, tissue samples were collected, snap frozen in liquid nitrogen and stored at -80 ºC. The average time gap between euthanasia and tissue collection was ~ 15 minutes, maximum time was 25 minutes. The tissues collected were hypothalamus (HYPO), adenohypophysis (AHYP), which was separated from the neurohypophysis, thyroid gland (THYG), gonads (GONA) from both sexes, and back fat tissue (FATB). The hypothalamus included the mamillary body and grey tubercle but excluded the chiasma opticum. Throughout this work, each sample was identified by the acronym of the tissue followed by the animal id, e.g., FATBLWF1 refers to back fat tissue from female 1 Large White.