A mRNA expression study has been performed 20-25 minutes postmortem obtained samples from Longissimus dorsi muscle of 59 Duroc x LD/LW pigs to search for gene sequences related to meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) or to meat composition (intramuscular fat, content of several fatty acid (C16:0, C18:0, C18:1 and C18:2), ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) traits in order to find targets for selection. Gene ontology analysis, biological pathways and gene networks studies all show, that many more differentially expressed genes (506 vs 279) are related to meat quality (Group P, or perimortem characters) than to meat composition traits (Group L, or whole life traits). The difference between the number of GO terms annotated, biological pathways and gene networks in groups P and L is notable due to the differences in the complexity of the generation process of P-traits and the involvement of other tissues or organs in the generation of variability of L-traits. Also, interactions between a list of differentially expressed genes were found in ECM-receptor interaction, TGF-beta signaling pathway, fatty acid elongation in mitochondria and adipocytokine signalling pathway indicating that a substantial fraction of the gene networks could be associated with interactions between differential expressed genes related to traits under study. A high number of the most overexpressed genes are related to muscle development and functionality and repair mechanisms; they could be good candidates for breeding programs whose main goal is to enhance meat quality.
Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle.
Age, Specimen part
View SamplesBackground. More than one million women in fertile age are infected with Trypanosoma cruzi worldwide. Anti-T.cruzi seropositivity in mothers has been associated with adverse pregnancy outcome but there is still a knowledge gap regarding this effect. Our aim was to compare the gene expression profile of term placental environment from T. cruzi seropositive (SP) and seronegative (SN) mothers. Methods. A RNA-Seq was performed in 9 pools of 2 different placental RNA samples each: 3 belonging to placentas from SN and 6 from SP. Each pool consisted of a binomial of a female/male newborn and a vaginal/caesarean delivery. None of the newborns resulted infected. Results. Only 42 genes showed a significant fold change between SP and SN groups. Among the down-regulated genes were KISS1 and CGB5. In the up-regulated genes group were: KIF12, HLA-G, PRG2, TAC3, FN1 and ATXN3L. To identify pathways significantly associated with maternal T. cruzi-infection, a gene-set association analysis was implemented. The placental environment transcriptomic profile of SP consisted of an enrichment in immunological genes sets (inflammatory response and lymphocytic activation were over-expressed) whereas numerous biosynthetic processes were down-regulated. Conclusions. It is worth noting that several differentially expressed genes in SP placentas code for proteins associated to preeclampsia and miscarriage. This first transcriptomics study in human term placental environment from non-infected deliveries shows a placental response that may affect the faetus while protecting it from the parasite infection; this host response could be responsible for the low rate of congenital transmission observed in human chronic Chagas disease. Background. More than one million women in fertile age are infected with Trypanosoma cruzi worldwide. Anti-T.cruzi seropositivity in mothers has been associated with adverse pregnancy outcome but there is still a knowledge gap regarding this effect. Our aim was to compare the gene expression profile of term placental environment from T. cruzi seropositive (SP) and seronegative (SN) mothers. Methods. A RNA-Seq was performed in 9 pools of 2 different placental RNA samples each: 3 belonging to placentas from SN and 6 from SP. Each pool consisted of a binomial of a female/male newborn and a vaginal/caesarean delivery. None of the newborns resulted infected. Results. Only 42 genes showed a significant fold change between SP and SN groups. Among the down-regulated genes were KISS1 and CGB5. In the up-regulated genes group were: KIF12, HLA-G, PRG2, TAC3, FN1 and ATXN3L. To identify pathways significantly associated with maternal T. cruzi-infection, a gene-set association analysis was implemented. The placental environment transcriptomic profile of SP consisted of an enrichment in immunological genes sets (inflammatory response and lymphocytic activation were over-expressed) whereas numerous biosynthetic processes were down-regulated. Conclusions. It is worth noting that several differentially expressed genes in SP placentas code for proteins associated to preeclampsia and miscarriage. This first transcriptomics study in human term placental environment from non-infected deliveries shows a placental response that may affect the faetus while protecting it from the parasite infection; this host response could be responsible for the low rate of congenital transmission observed in human chronic Chagas disease. Overall design: Serodiagnosis of pregnant women was done by means of conventional serological methods and carried out by the respective health centres based on routine assays. In maternal and umbilical cord blood samples T. cruzi presence was tested using multiplex Real Time PCR as previously described [6]. Maternal infection with other pathogens that produce congenital transmission and adverse pregnancy outcome were considered as exclusion criteria, as well as missing data or incorrect sampling. Fresh normal placentas were obtained after labour from vaginal or caesarean deliveries and placed within 24 hours at 4°C. Each placenta was dissected and the middle section [7] at 2 cm distance from the umbilical cord was isolated and placed into RNAlater solution (Applied Biosystems, Foster City, CA). Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80°C until used. Transcriptomic studies. A RNA-Seq experiment was done in 9 pools of 2 different placental RNA samples each: 3 pools (C1, C2 and C3) belonging to placentas from seronegative mothers (SN) and 6 pools (TC4 to TC9) from seropositive mothers (SP). Each pool consisted of a binomial of a female/male newborn and a vaginal/caesarean delivery. The cDNA Libraries were prepared according to Illumina''s TruSeq Stranded Total RNA with Ribo-Zero Gold for Human and a Hiseq 2.500 Illumina platform with 100 bp paired-end reads was used for sequencing
Alterations in Placental Gene Expression of Pregnant Women with Chronic Chagas Disease.
Subject
View SamplesHigh-fat diets are associated with increased obesity and metabolic disease in mice and humans. Here we used analysis of variance (ANOVA) to scrutinize a microarray data set consisting of 10 inbred strains of mice from both sexes fed atherogenic high-fat and control chow diets. An overall F-test was applied to the 40 unique groups of strain-diet-sex to identify 15,288 genes with altered transcription. Bootstrapping k-means clustering separated these changes into four strain-dependent expression patterns, including two sex-related profiles and two diet-related profiles. Sex-induced effects correspond to secretion (males) or fat and energy metabolism (females), whereas diet-induced changes relate to neurological processes (chow) or immune response (high-fat). The full set of pairwise contrasts for differences between strains within sex (90 different statistical tests) uncovered 32,379 total changes. These differences were unevenly distributed across strains and between sexes, indicating that strain-specific responses to high-fat diet differ between sexes. Correlations between expression levels and 8 obesity-related traits identified 5,274 associations between transcript abundance and measured phenotypic endpoints. From this number, 2,678 genes are positively correlated with total cholesterol levels and associate with immune-related categories while 2,596 genes are negatively correlated with cholesterol and connect to cholesterol synthesis.
Practical applications of the bioinformatics toolbox for narrowing quantitative trait loci.
Sex
View SamplesOver activation of the aryl hydrocarbon receptor (AhR) by TCDD results ampng other phenotypes in severe thymic atrophy accompanied by immunosuppression. The link between thymic atrophy, skewed thymocyte differntiation and immunosuppression is still not fully resolved. This study investigates the TCDD elicted exprssion changes in the ET, cortical thymus epithelial cell line.
Promoter analysis of TCDD-inducible genes in a thymic epithelial cell line indicates the potential for cell-specific transcription factor crosstalk in the AhR response.
Treatment, Time
View SamplesPlastids emit signals that broadly affect cellular processes. Based on previous genetic analyses, we propose that plastid signaling regulates the downstream components of a light signaling network and that these interactions coordinate chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light-regulated and plastid-regulated transcriptomes. We found that the plastid is a major regulator of light signaling, attenuating the expression of more than half of all light-regulated genes in our dataset and changing the nature of light regulation for a smaller fraction of these light-regulated genes.
Plastids are major regulators of light signaling in Arabidopsis.
Age, Specimen part
View SamplesIdentify genes that are differentially regulated as a consequence of restoration of full-length functional APC in a colorectal cancer cell lines. Overall design: Examine mRNA expression level changes between SW480 (APC defective) and SW480+APC (SW480 cells with restored functional APC) cells, whilst accounting for any non-specific expression changes by comparison to SW480+control vector.
Differential RNA-seq analysis comparing APC-defective and APC-restored SW480 colorectal cancer cells.
No sample metadata fields
View SamplesHigh quality genetic material is an essential pre-requisite when analyzing gene expression using microarray technology. Peripheral blood mononuclear cells (PBMC) are frequently used for genomic analyses, but several factors can affect the integrity of nucleic acids prior to their extraction, including the methods of PBMC collection and isolation. In this study, we compared the Ficoll-Paque density gradient centrifugation and BD Vacutainer cell preparation tube (CPT) protocols to determine if either method offered a distinct advantage in preparation of PBMC-derived immune cell subsets for their use in gene expression analysis. We compared gene expression in PBMC and individual immune cell types from Ficoll and CPT isolation protocols using Affymetrix microarrays.
Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient.
Specimen part
View SamplesWe report the application of ultrashort metabolic labeling of RNA for high-throughput profiling of RNA processing in Drosophila S2 cells. Overall design: Examination of 3 different labeling timepoints in Drosophila S2 cells.
The kinetics of pre-mRNA splicing in the <i>Drosophila</i> genome and the influence of gene architecture.
Cell line, Subject
View SamplesGobal expression analysis in four somatic tissues (brain, liver, kidney and muscle) of adult 40,XX and 39,XO mice with the aim of identifying which genes are expressed from both X chromosomes as well as those genes deregulated in X chromosome monosomy.
Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome.
Sex, Age, Specimen part
View SamplesThis study compares the gene expression changes in Sus scrofa in response to two different methods for abdominal surgical incisions ; electrosurgery and harmonic blade.
Ultrasonic incisions produce less inflammatory mediator response during early healing than electrosurgical incisions.
Specimen part, Treatment
View Samples