Pig brain miRNA profiling
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE148302 | GEO | 2020/12/01
REPOSITORIES: GEO
Similar Datasets
Project description:Purpose: The aim of present research was to identify miRNAs potentially related with muscle growth in pig Methods: miRNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Based on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The miRNA libraries were constructed form total RNA with the use Neb Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the protocol. The quantification of obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies) and a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). The miRNA-seq was performed in 36 single-end cycles on HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Differentially expressed microRNAs were detected using the DESeq2 software while validation was performed by qPCR. Results: miRNA-seq approach allowed to identify 196 known and 149 potentially novel miRNAs in both breeds. The comparison of miRNA profiles between pig groups with different loin weight showed differential expression of 57 microRNAs for Hampshire pigs and 34 miRNAs for Pietrain pigs. Furthermore, 18 common microRNAs with differential expression were identified for both breeds tested. The Gene Ontology analysis (DIANA mirPath v.3 tool) confirmed that detected genes were involved in regulation of cell cycle, fatty acid biosynthesis, regulation of actin cytoskeleton, lysine degradation and ubiquitin mediated proteolysis. According to the KEGG Database, these DE miRNAs enrich the following pathways, i.a.: the Hippo signaling pathway, TGF-beta signaling pathway and PI3K-Akt signaling pathway. Conclusions: Obtained results allow to propose the panel of miRNAs, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate miRNAs related with important production traits in pigs.
2018-04-23 | GSE109215 | GEO
Project description:Poor maternal nutrition causes intrauterine growth restriction (IUGR); however, its effects on fetal cardiac development are unclear. We have developed a baboon model of moderate maternal undernutrition, leading to IUGR. We hypothesized that the IUGR affects fetal cardiac structure and metabolism. Six control pregnant baboons ate ad-libitum (CTRL)) or 70% CTRL from 0.16 of gestation (G). Fetuses were euthanized at C-section at 0.9G under general anesthesia. Male but not female IUGR fetuses showed left ventricular fibrosis inversely correlated with birth weight. Expression of extracellular matrix protein TSP-1 was increased (p<0.05) in male IUGR. Expression of cardiac fibrotic markers TGFß, SMAD3 and ALK-1 were downregulated in male IUGRs with no difference in females. Autophagy was present in male IUGR evidenced by upregulation of ATG7 expression and lipidation LC3B. Global miRNA expression profiling revealed 56 annotated and novel cardiac miRNAs exclusively dysregulated in female IUGR, and 38 cardiac miRNAs were exclusively dysregulated in males (p<0.05). Fifteen (CTRL) and 23 (IUGR) miRNAs, were differentially expressed between males and females (p<0.05) suggesting sexual dimorphism, which can be at least partially explained by differential expression of upstream transcription factors (e.g. HNF4a, and NF?B p50). Lipidomics analysis of fetal cardiac tissue exhibited a net increase in diacylglycerol and plasmalogens and a decrease in triglycerides and phosphatidylcholines. In summary, IUGR resulting from decreased maternal nutrition is associated with sex-dependent dysregulations in cardiac structure, miRNA expression, and lipid metabolism. If these changes persist postnatally, they may program offspring for higher later life cardiac risk.
2018-04-30 | MTBLS426 | MetaboLights
Project description:Purpose: Analysis of the effect of different fats and amonut of cDDGS in the feedstuff on miRNA expression in porcine backfat Methods: miRNA-seq analysis was performed on backfat samples collected from 24 male and female crossbred fatteners originating from sows (Polish Landrace × White Large Polish) mated with a boar (Duroc × Pietrain) divided into four dietary groups: 7-cDDGS+rapeseed oil (group I), n=6 (+cDDGS+rapeseed oil -group II), n= 6 (+cDDGS+beeftallow -group III),n=5 (+cDDGS+coconut oil -group IV). The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 100 single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between dietary groups were identified with the DESeq2 software. Results: The comparison of miRNA profiles between dietary groups showed The highest number of miRNAs with altered expression was identified in the comparison of animals fed the diet containing cDDGS and coconut oil (group IV) with animals from the –cDDGS + rapeseed oil (group I) (37 miRNA, p adjusted <0.01). Moreover, in comparison between the group IV and groups III and II , 29 (12 upregulated and 17 downregulated in +cDDGS+coconut oil group) and 28 (10 upregulated and 18 downregulated in +cDDGS+coconut oil group) miRNAs were identified, respectively (p adjusted <0.1) Conclusions: Obtained results suggest that coconut oil induces changes in miRNA profile of backfat in pigs.
2021-09-17 | GSE184177 | GEO
Project description:Purpose: The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphy lococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing. Methods: miRNA-seq analysis was performed on mammary gland parenchyma samples collected from non-infected cows and those infected with coagulase-positive or -negative staphylococci. The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). Single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between investigated groups were identified with the DESeq2 software. Results: Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identifed, including 32 that were diferentially expressed (p≤0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identifed: 10 were upregulated (p≤0.05), and 2 downregulated (p≤0.05). Comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identifed; in both comparisons, diferentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identifed in each comparison, with 2 being common to both immune system processes and signal transduction. Conclusions: Obtained results enabled us to characterize the miRNA profile of the mammary gland parenchyma tissue, not only the healthy one but also the tissue infected with coagulase-positive and negative staphylococci as well as allowed identification of miRNAs differing the examined groups and characteristic for the staphylococci infection. They also indicated that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).
2021-04-14 | GSE172013 | GEO
Project description:Purpose: The aim of present research was to identify genes potentially related with muscle growth in pig Methods: RNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire. Base on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The cDNA libraries were constructed form 300 ng of total RNA with the use TruSeq RNA Sample Prep Kit v2 kit (Illumina) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 101 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR. Results: RNA-seq approach allowed to identify 627 and 416 DEGs between pig groups with different loin weight (pvalue <0.05; fold change≤1.5) for Pietrain and Hampshire; respectively. Next, the comparison of obtained genes sets showed 43 genes identified in both breeds. The Gene Ontology analysis (Panther software) confirmed that detected genes were involved in regulation of metabolic process (18 genes), developmental growth or skeletal system development (PCOLCE; BBS2; TBX2; RBBP6; ATAF5). According to David software these genes belong to PI3K-Akt signaling, Focal adhesion and ECM-receptor interaction pathways. Conclusions: Obtained results allow to propose the panel of genes, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate genes related with important production traits in pigs.
2017-12-01 | GSE107207 | GEO
Project description:Purpose: The aim of present research was to identify miRNAs potentially related with fattness traits in pigs Methods: miRNA-seq analysis was performed on subcutaneous fat samples collected from 22 pigs representing two sire-line breeds – Pietrain and Hampshire and one dam-line – Large White. Based on dissection data, pigs were selected from a larger population in terms of fatness traits to obtain the most extreme groups in each breed. The cDNA libraries were constructed form 300 ng of total RNA with the use NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, United States) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 36 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR. Results: RNA-seq approach allowed to identify miRNAs differentially expressed between pigs with various fatness traits in each analyzed breeds: 64 for Pietrain pigs; 41 for Hampshire and 46 for Large White pigs (pvalue <0.05; fold change≤1.5). The comparison of obtained miRNAs sets showed 13 miRNAs identified in all three breeds. The Gene Ontology analysis (mirPath v.3.0 DIANA Tools web with DIANA—TarBase v7.0 as a reference) confirmed that detected miRNAs were involved in fatty acid biosynthesis (pvalue <1e-325); fatty acid metabolism (pvalue 6.661338e-16); ECM-receptor interaction (pvalue <1e-325). The most important targeted genes regulated by identified miRNAs were: fatty acid synthase – FASN; Acetyl-CoA carboxylase 1 – ACACA; Malonyl CoA-acyl carrier protein transacylase – MCAT and acetyl-CoA acyltransferase 1 and 2 (ACAA1 and ACAA2 genes). Conclusions: Obtained results allow to propose the panel of miRNAs, which can be related with fatness in pig. Such analysis can be the basis of future research in terms of identification of molecular mechanisms related with adipogenesis and fatness traits in pigs.
2018-11-22 | GSE122816 | GEO
Project description:The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut and liver sequencing was done in male and female separately. Majority of the sequenced reads (16-62%) mapped to known miRNAs, with the exception of ovary (5.7%) and testis (7.8%). Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%). The prediction tool identified a total of 459 novel pre-miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated (22) and sex associated (34) miRNAs, respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30% seed homology to human miRNA) as a genomic resource which can facilitate further investigations to understand miRNA-mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Known miRNA profiling, novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish (in triplicate) was carried out using the Illumina HiSeq 2000 platform.
2015-10-16 | E-GEOD-57169 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to compare the microRNA transcriptomes of four high-altitude vertebrates and their low-altitude relatives for six organs (heart,liver,spleen,lung,kidney and muscle). Methods: Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were humanely killed to ameliorate suffering. A piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were used to extract total RNA. Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit and sequenced on the Illumina HiSeq 2500. The raw data were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Results: we detected 2,036 mature miRNAs in five species and identified 49 orthologues among vertebrate, 111 orthologues in artiodactyla and 171 orthologues in ruminant . Conclusions: We identified comparable numbers of miRNAs in each species.
2019-08-19 | GSE124418 | GEO
Project description:Purpose: The goals of this study are to compare genes change between FBXW7f/f and LysM-cre FBXW7f/f BMDM after LPS treatment Methods: BMDM mRNA from 6-8weeks FBXW7f/f (WT) and LysM-cre FBXW7f/f (KO) mice were generated by transcription sequencing, using Illumina. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
2020-02-20 | GSE125242 | GEO
Project description:<p>We have deeply sequenced total RNA and whole exome of six different post-mortem human snap-frozen tissues (brain, liver, lung, striated muscle, kidney, heart) from three unrelated healthy Caucasian individuals (males, aged 47-54) with the aim to characterize post-transcriptional events due to alternative splicing and RNA editing. In addition, to facilitate the detection of RNA editing sites we have also resequenced the entire genome of each individual. Data are also used to investigate tissue-specific abundance of mitochondrial DNA from exomes and its correlation with mitochondrial transcription, mass and respiratory activity.</p> <p>Tissues were obtained from Cureline (South San Francisco, CA, USA). DNA and RNA were purified using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) and the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), respectively.</p> <p>Exome capture was performed using the TruSeq Exome Enrichment Kit (Illumina, San Diego, CA) and the sequencing was carried out at IGA Technology Services in Udine (Italy) on Illumina HiSeq 2000 (generating for each tissue approximately 40 millions of 100bp paired-end reads). </p> <p>Strand-oriented RNA reads (2x100bp) were generated using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, USA) and sequenced at IGA Technology Services in Udine (Italy) on Illumina HiSeq 2000 platform.</p> <p>Whole genome resequencing was performed at Personal Genomics in Italy on an Illumina HiSeq 2000 platform (2x100bp) with a mean coverage of 30X.</p> <p>MiRNA-Seq was instead performed at IBBE Institute (Italy) using the TruSeq Small RNA Sample Prep Kit on Illumina MiSeq platform.</p> <p>Preliminary bioinformatics analyses have been performed to check quality using FASTQC software and inconsistent read regions have been trimmed using trim_galore. All reads were mapped onto the human reference genome (version hg19) using GSNAP.</p>
| phs000870 | dbGaP