Similar Datasets
Project description:RNA-seq analysis of perichondral tissues obtained from rabbit
| PRJNA1336055 | ENA
Project description:RNA-Seq analysis carried out in three different backcrosses based on Iberian breed with Landrace, Pietrain and Duroc breeds
2017-10-31 | PRJEB23068 | EVA
Project description:Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including SOX17, ANXA4, DLX3, DMRT1, FLNB, IRF6, CBFA2T2, TFCP2L1, EFNA5, SLIT2, and CYFIP2, with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, ANXA4, CBFA2T2, and TFCP2L1, which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.
| S-EPMC10573446 | biostudies-literature
Project description:Glycogenes regulate a wide array of biological processes in the development of organisms as well as different diseases such as cancer, primary open-angle glaucoma, and renal dysfunction. The objective of this study was to explore the role of differentially expressed glycogenes (DEGGs) in three major tissues such as brain, muscle, and liver using mouse RNA-seq data, and we identified 579, 501, and 442 DEGGs for brain versus liver (BvL579), brain versus muscle (BvM501), and liver versus muscle (LvM442) groups. DAVID functional analysis suggested inflammatory response, glycosaminoglycan metabolic process, and protein maturation as the enriched biological processes in BvL579, BvM501, and LvM442, respectively. These DEGGs were then used to construct three interaction networks by using GeneMANIA, from which we detected potential hub genes such as PEMT and HPXN (BvL579), IGF2 and NID2 (BvM501), and STAT6 and FLT1 (LvM442), having the highest degree. Additionally, our community analysis results suggest that the significance of immune system related processes in liver, glycosphingolipid metabolic processes in the development of brain, and the processes such as cell proliferation, adhesion, and growth are important for muscle development. Further studies are required to confirm the role of predicted hub genes as well as the significance of biological processes.
| S-EPMC4121153 | biostudies-literature
Project description:Rodent models have been widely used as analogs for estimating spaceflight-relevant molecular mechanisms in human tissues. NASA GeneLab provides access to numerous spaceflight omics datasets that can potentially generate novel insights and hypotheses about fundamental space biology when analyzed in new and integrated fashions. Here, we performed a pilot study to elucidate space biological mechanisms across tissues by reanalyzing mouse RNA-sequencing spaceflight data archived on NASA GeneLab. Our results showed that clock gene expressions in spaceflight mice were altered compared with those in ground control mice. Furthermore, the results suggested that spaceflight promotes asynchrony of clock gene expressions between peripheral tissues. Abnormal circadian rhythms are associated not only with jet lag and sleep disorders but also with cancer, lifestyle-related diseases, and mental disorders. Overall, our findings highlight the importance of elucidating the causes of circadian rhythm disruptions using the unique approach of space biology research to one day potentially develop countermeasures that benefit humans on Earth and in space.
| S-EPMC7555136 | biostudies-literature
Project description:Background: Septic shock is a life-threatening clinical condition characterized by a robust immune inflammatory response to disseminated infection. Little is known about its impact on the transcriptome of distinct human organs. Objective and Methods: To address this, we performed RNA sequencing of samples from the prefrontal cortex, hippocampus, heart, lung, kidney and colon of seven individuals who succumbed to sepsis and seven uninfected controls. Main Results: We identified that the lungs and colon were the most affected organs. While gene activation dominated, strong inhibitory signals were also detected, particularly in the lungs. Principal Conclusions: We found that septic shock is an extremely heterogeneous disease, not only when different individuals are investigated, but also when comparing different tissues of the same patient. However, several pathways, such as respiratory electron transport and other metabolic functions, revealed distinctive alterations, providing evidence that tissue specificity is a hallmark of sepsis. Strikingly, we found evident signals of accelerated ageing in our sepsis population.
2023-09-21 | GSE237861 | GEO
Project description:Due to heterogeneous multifocal nature of prostate cancer (PCa), there is currently a lack of biomarkers that stably distinguish it from benign prostatic hyperplasia (BPH), predict clinical outcome and guide the choice of optimal treatment. In this study RNA-seq analysis was applied to formalin-fixed paraffin-embedded (FFPE) tumor and matched normal tissue samples collected from Russian patients with PCa and BPH. We identified 3384 genes differentially expressed (DE) (FDR < 0.05) between tumor tissue of PCa patients and adjacent normal tissue as well as both tissue types from BPH patients. Overexpression of four of the discovered genes (ANKRD34B, NEK5, KCNG3, and PTPRT) was validated by RT-qPCR. Furthermore, the enrichment analysis of overrepresented microRNA and transcription factor (TF) recognition sites within DE genes revealed common regulatory elements of which 13 microRNAs and 53 TFs were thus linked to PCa for the first time. Moreover, 8 of these TFs (FOXJ2, GATA6, NFE2L1, NFIL3, PRRX2, TEF, EBF2 and ZBTB18) were found to be differentially expressed in this study making them not only candidate biomarkers of prostate cancer but also potential therapeutic targets.
| S-EPMC5464844 | biostudies-literature
Project description:BackgroundQualitative and quantitative analysis of small non-coding RNAs by next generation sequencing (smallRNA-Seq) represents a novel technology increasingly used to investigate with high sensitivity and specificity RNA population comprising microRNAs and other regulatory small transcripts. Analysis of smallRNA-Seq data to gather biologically relevant information, i.e. detection and differential expression analysis of known and novel non-coding RNAs, target prediction, etc., requires implementation of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. As a consequence, the analytical workflow is slowed down by the need for continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once.ResultsWe designed a novel modular pipeline (iMir) for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. As statistics is crucial in deep-sequencing data analysis, we devised and integrated in iMir tools based on different statistical approaches to allow the operator to analyze data rigorously. The pipeline created here proved to be efficient and time-saving than currently available methods and, in addition, flexible enough to allow the user to select the preferred combination of analytical steps. We present here the results obtained by applying this pipeline to analyze simultaneously 6 smallRNA-Seq datasets from either exponentially growing or growth-arrested human breast cancer MCF-7 cells, that led to the rapid and accurate identification, quantitation and differential expression analysis of ~450 miRNAs, including several novel miRNAs and isomiRs, as well as identification of the putative mRNA targets of differentially expressed miRNAs. In addition, iMir allowed also the identification of ~70 piRNAs (piwi-interacting RNAs), some of which differentially expressed in proliferating vs growth arrested cells.ConclusionThe integrated data analysis pipeline described here is based on a reliable, flexible and fully automated workflow, useful to rapidly and efficiently analyze high-throughput smallRNA-Seq data, such as those produced by the most recent high-performance next generation sequencers. iMir is available at http://www.labmedmolge.unisa.it/inglese/research/imir.
| S-EPMC3878829 | biostudies-literature
Project description:The rabbit has great commercial importance as a source of meat and fur, as well as its uses as a laboratory animal for the production of antibodies, used to detect the presence or absence of disease and for research in infectious diseases and immunology. One of the most critical problems in immunology is to understand how the immune system detects the presence of infectious agents and disposes the invader without destroying the self-tissues. Genetic characterization of Toll-like receptors has established that innate immunity is a skillful system that detects invasion of microbial pathogens. Our work aimed to identify, clone and express the Oryctolagus cuniculus (rabbit) TLR-1 mRNA and its encoding protein. We cloned the complete mRNA sequence of Oryctolagus cuniculus TLR-1 and deposit it in the GenBank under accession number (KC349941), which has 2388 base pair and it encodes encode an open reading frame (ORF) translated into 796 amino acids mRNA and consist of 20 types of amino acids. The analysis of amino acid sequence revealed that the rabbit TLR-1 has a typical protein components belonging to the TLR family. Rabbit TLR-1 was expressed in a wide variety of rabbit tissues, which indicate an important role in immune system in different organs.
| S-EPMC5099378 | biostudies-literature
Project description: Not available
| S-BSST1277 | biostudies-other