Ontology highlight
ABSTRACT:
PROVIDER: PRJNA816314 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18330000.fastq.gz | Fastqsanger.gz | |||
| SRR18330001.fastq.gz | Fastqsanger.gz | |||
| SRR18330002.fastq.gz | Fastqsanger.gz | |||
| SRR18330003.fastq.gz | Fastqsanger.gz | |||
| SRR18330004.fastq.gz | Fastqsanger.gz |
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Project description:Both bacterial and viral diseases are a major threat to farmed fish, as well as wild fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of virus dsRNA, and RNA sequencing was performed. Immune genes were identified, and transcriptome-wide analyses of early immune responses in lumpfish leukocytes showed that 310 and 1872 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of differentially expressed genes (DEGs) showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, MDA5, TRIM25, STING, as well as IRF3, IL-8 and TNFα. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Our analyses unravel the innate immune pathways playing a major role in antiviral defence in lumpfish. The information gathered can be used to compare research findings and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar).
2023-06-01 | E-MTAB-12884 | biostudies-arrayexpress
Project description:The implantation of deep brain stimulation (DBS) electrodes into the human brain is a neurosurgical treatment for, e.g., movement disorders. We describe a novel approach to collecting brain tissue from DBS surgery-guiding instruments for liquid chromatography-mass spectrometry and RNA sequencing analyses. Proteomics and transcriptomics showed that the approach is useful for obtaining disease-specific expression data. A comparison between our improved and the previous approaches and related datasets was performed. BioStudies:https://www.ebi.ac.uk/biostudies/studies/S-BSST667 and Publication: https://www.biorxiv.org/content/10.1101/2021.06.18.448926v1
2021-06-29 | PXD026936 | Pride
Project description:Typical multiomics studies employ separate methods for DNA, RNA, and protein sample preparation, which is labor intensive, costly, and prone to sampling bias. We describe here a method for preparing high-quality DNA, RNA, and protein or peptides for whole genome sequencing, RNA sequencing, and whole proteome analysis from a single sample. This method utilizes a reversible protein tagging scheme to covalently link all proteins in a lysate to a bead-based matrix and nucleic acid precipitation and selective solubilization to yield separate pools of protein and nucleic acids. The proteins are then digested to generate peptides ready for mass spectrometric proteome analysis. We demonstrate the utility of this method to compare the genomes, transcriptomes, and proteomes of four triple-negative breast cancer cell lines with different degrees of malignancy. These data show the involvement of both RNA and associated proteins, and protein-only dependent pathways that distinguish these cell lines. We also demonstrate the utility of this multiomics workflow for tissue analysis using mouse brain, liver and lung tissue.
2023-08-29 | MSV000092780 | MassIVE
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Background: The majority of multi-omics studies make use of adjacent fresh-frozen tissue pieces for different analyses. This approach however is not considering the intrinsic tissue heterogeneity and can lead to a biological mismatch of different omics layers. To overcome this limitation, we here propose an alternative approach where tissue is cryogenically pulverized and lyophilized, obtaining a homogenous tissue powder that can be used for subsequent omics studies. The purpose of this study was to investigate how omics analysis differ or coincide when comparing adjacent tissue slices to homogenized powder using three major mammalian organs from a wildtype mouse model.
Methods: Healthy fresh-frozen and pulverized-lyophilized mouse tissue from brain, kidney, and liver was subjected to DNA methylation and genome sequencing (genomics), RNA sequencing (transcriptomics), protein (proteomics), and metabolite (metabolomics) analysis. Obtained analytical results were investigated by statistical and quality control measures, including dendrograms, correlation analysis, principal component analysis, RNA integrity, feature coverage, and energy charge estimation.
Results: DNA methylation was not affected differently by the two different tissue processing methods. The RNA integrity obtained was comparable between fresh-frozen tissue slicing and pulverization-lyophilization. The coverage of gene transcripts, proteins, and metabolites was preserved similarly by both methodological approaches. Overall the pulverization-lyophilization approach resulted in a reduced heterogeneity between biological replicates.
Conclusions: Cryogenically pulverized and lyophilized tissue preserves the most important cellular molecular features, such as RNA integrity, DNA methylation status, gene transcript, protein, and metabolite coverage. Therefore, it is a suitable alternative method for improved multi-omics analysis, providing reduced sample heterogeneity, beneficial for batch reproducibility, as well as easier transportation and storage conditions due to complete water removal.
2024-03-11 | MSV000094288 | GNPS
Project description:Framingham Heart Study RNA sequencing in postmortem brain tissue
| PRJNA763280 | ENA