HMSCs were cultured in DMSO-containing medium for 48 hours, and RNA was extracted for transcriptome sequencing
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens (human)
SUBMITTER:
PROVIDER: S-BSST1969 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description: Not available
| S-BSST1970 | biostudies-other
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| S-BSST1735 | biostudies-other
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| S-BSST1738 | biostudies-other
Project description:To understand the effect of DMSO in preimplantation embryos, we have treated mouse 1 cell zygotes with DMSO and found that DMSO treatment caused 2 or 4 cell embryonic arrest and altered the acetylation levels of mouse preimplantation embryos To illustrate the mechanism of DMSO in mouse preimplantation embryos, fertilized zygotes have been treated with 2% of DMSO and then performed RNA-seq analyses. Differentially expressed genes were identified using DESeq2 after adjustment for false discovery rate (FDR q value < 0.05). Gene Set Enrichment Analysis (GSEA) was also performed to identify biological pathways significantly modulated by DMSO. Raw and processed RNA-seq data were deposited and made publicly available on the Gene Expression Omnibus (GEO; GSE124598). The data presented in this article are related to the research paper entitled "DMSO impairs the transcriptional program for maternal-to-embryonic transition by altering histone acetylation", available in Biomaterials [1].
| S-EPMC6940686 | biostudies-literature
Project description:Duck hepatitis A virus 3 (DHAV-3), the only member of the novel genus Avihepatovirus, in the family Picornaviridae, can cause significant economic losses for duck farms in China. Reports on the pathogenicity and the antiviral molecular mechanisms of the lethal DHAV-3 strain in ducklings are inadequate and remain poorly understood. We conducted global gene expression profiling and screened differentially expressed genes (DEG) of duckling liver tissues infected with lethal DHAV-3. There were 1643 DEG and 8979 DEG when compared with mock ducklings at 12 hours post-infection (hpi) and at 48 hpi, respectively. Gene pathway analysis of DEG highlighted mainly biological processes involved in metabolic pathways, host immune responses, and viral invasion. The results may provide valuable information for us to explore the pathogenicity of the virulent DHAV-3 strain and to improve our understanding of host-virus interactions.
| S-EPMC6011267 | biostudies-literature
Project description:Next-generation sequencing (NGS)-based mutation panels profile multiple genes simultaneously, allowing the reporting of numerous genes while saving labor and resources. However, one drawback of using NGS is that the turnaround time is often longer than conventional single gene tests. This delay can be problematic if molecular results are required to guide therapy in patients with clinically aggressive diseases, such as acute myeloid leukemia. To overcome this limitation, we developed a novel custom platform designated as Ultra-rapid Reporting of GENomic Targets (URGENTseq), an integrated solution that includes workflow optimization and an innovative custom bioinformatics pipeline to provide targeted NGS results on fresh peripheral blood and bone marrow samples within an actionable time period. URGENTseq was validated for clinical use by determining mutant allelic frequency and minimum coverage in silico to achieve 100% concordance for all positive and negative calls between the URGENTseq and conventional sequencing approach. URGENTseq enables the reporting of selected genes useful for immediate diagnosis (CALR, CSF3R, JAK2, KRAS, MPL, NPM1, NRAS, SF3B1) and treatment decisions (IDH1, IDH2) in hematologic malignancies within 48 hours of specimen collection. In addition, we summarize the molecular findings of the first 272 clinical test results performed using the URGENTseq platform.
| S-EPMC11773613 | biostudies-literature
Project description:Mammalian injury responses are characterized by fibrosis and scarring rather than functional regeneration. Limited regenerative capacity in mammals could reflect a loss of pro-regeneration programs or active suppression by genes functioning akin to tumor suppressors. To uncover programs governing regeneration in mammals, we performed comprehensive transcript screening in human subjects after laser rejuvenation treatment and cross-referenced these transcripts to those found in mice with enhanced Wound Induced Hair Neogenesis (WIHN), a rare example of mammalian organogenesis1,2. We find the anti-viral endoribonuclease RNase L to be a powerful suppressor of regeneration. Rnasel-/- mice exhibit remarkable regenerative capacity, with elevated WIHN through enhanced IL-36α. Consistent with the known role of RNase L to stimulate caspase-1, we find that pharmacologic inhibition of caspases promotes regeneration in a novel IL-36-dependent manner. Additionally, these responses are not limited to skin but extend to other organs, such as the colon, suggesting that suppression of regeneration is a fundamental characteristic of epithelial wound healing. Taken together, this work suggests that RNase L functions as a regeneration repressor gene in a functional tradeoff that prioritizes host antiviral abilities and is a target to enhance healing in multiple epithelial organs, perhaps even during viral infection.
2025-01-01 | GSE164667 | GEO
Project description:To investigate whether Aramchol might reduce liver fibrosis in part directly inhibiting HSCs, we treated LX-2 cells with Aramchol, 10 µM for 24 or 48 hours, then performed RNA sequencing. Sequencing libraries were made with the TruSeq Stranded mRNA Library Prep Kit by manufacturers suggestions. Sequencing parameters are as follows: poly-A RNA enrichment, 175 bp paired reads ran on HiSeq2500 Illumina instrument. Mapping of raw sequencing reads was performed using STAR (2.4.0c) to the UCSC GRCh37/hg19 reference genome.
2021-05-19 | E-MTAB-9870 | biostudies-arrayexpress
Project description:Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology. These samples were analyzed with 16S rRNA gene sequencing, inferred gene function profiles, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics through the Qiita, PICRUSt, and GNPS pipelines, respectively. The human sample microbiomes clustered with the corresponding sample types in the American Gut Project (http://www.americangut.org), and the fermented food samples produced a separate cluster. The microbial communities of the household surfaces were primarily sourced from the fermented foods, and their consumption was associated with increased gut microbial diversity. Untargeted metabolomics revealed that human skin and fermented food samples had separate chemical ecologies and that stool was more similar to fermented foods than to other sample types. Metabolites from the fermented foods, including plant products such as procyanidin and pheophytin, were present in the skin and stool samples of the individuals consuming the foods. Some food metabolites were modified during digestion, and others were detected in stool intact. This study represents a first-of-its-kind analysis of multi-omics data that achieved time intervals matching those of classic microbiological culturing. IMPORTANCE Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology.
| S-EPMC5069746 | biostudies-literature