Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10293913_1.fastq.gz | Fastqsanger.gz | |||
| SRR10293913_2.fastq.gz | Fastqsanger.gz | |||
| SRR10293914_1.fastq.gz | Fastqsanger.gz | |||
| SRR10293914_2.fastq.gz | Fastqsanger.gz | |||
| SRR10293915_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: We evaluated T. rubrum transcriptome using high-throughput RNA-sequencing (RNA-seq) technology aiming to identify metabolic pathways modulated by the antidepressive sertraline. Methods: We employed the next-generation sequencing (RNA-seq) approach to identify the central responsively genes related to SRT effects. Results: we identified the main effects of sertraline as the disturbance of maintaining the fungal cell wall and plasmatic membrane stability targeting ergosterol biosynthesis. SRT also modulated genes encoding enzymes related to fungal energy metabolism, cellular detoxification, and defense against oxidative stress Conclusions: Our findings provide insights into a specific molecular network interaction operative for main-taining metabolic stability perturbed by SRT drug showing relevant targets for its strategic use in the dermatophytosis field.
2023-02-23 | GSE218521 | GEO
Project description:Study identifying transcriptional differences present between C57BL/6J and B6;129-Gaatm1Rabn/J mice, or driven by Enzyme Replacement Therapy (ERT), Substrate Reduction Therapy (SRT), or Both, administered to the mutant strain. All expression profiles were assessed in bulk gastrocnemius muscle collected from 18-21 week-old mice that had been provided with chow formulated with vehicle (veh.), MZ-101 (SRT), or alglucosidase alfa 20mg/kg biweekly (ERT) for 12 weeks.
2024-01-01 | GSE208215 | GEO
Project description:To test whether a genomic classifier (GC) predicts development of metastatic disease in patients treated with salvage radiation therapy (SRT) after radical prostatectomy (RP).
2017-04-04 | GSE79915 | GEO
Project description:The aim of the present work was to maximise NO2- conversion over NO3- reduction coupled with complete sulphide (HS-) oxidation, by the selective control of influent S/N ratio and sludge retention time (SRT). A 2.5-L chemostat was operated for 115 days and three operational phases were tested at decreasing SRT of 40, 23 and 13 h, testing S/N ratios in the range of 0.5-1 gS/gN. Successful sulphide-driven PAD was achieved and lead to average NO2- conversion efficiencies as high as 77±17% at all the conditions tested, with the highest value of 99% at the lowest S/N of 0.58 gS/gN and SRT of 23 h. Respirometric tests showed that NO3- uptake rate was stable at 90±10 mgN/gVSS/h, either when NO3- was present as sole electron acceptor or at NO2- levels as high as 120 mgN/l; on the contrary, NO2- uptake rates were very sensitive to the applied conditions. Metabarcoding analyses revealed that the microbial community was highly enriched in Sulphur Oxidizing Bacteria (SOB>80%) and strict and stable S-limiting conditions appeared to favour Thiobacillus over Sulfurimonas genus. A preliminary assessment of N2O potential emission was also performed. To the best of our knowledge, this is the first work evaluating the synergic effect of SRT and influent S/N ratio on nitrite accumulation in highly SOB-enriched systems and the NO2- conversion efficiencies achieved are among the highest reported in literature.
2022-12-21 | GSE192713 | GEO
Project description:Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of unbiased SRT methods targeting the polyA tail of mRNA, relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available SRT assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), an SRT workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we demonstrate the RRST protocol on tissue sections collected from five challenging tissue types, including: human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyzed 52 tissue sections and our results demonstrate that RRST is a versatile, powerful, and reproducible protocol for FF specimens of different qualities and origins.
2022-12-25 | GSE221571 | GEO
Project description:Most lysosomal storage diseases (LSDs) have a significant neurological component, including types 2 and 3 Gaucher disease (neuronal forms of Gaucher disease; nGD). No therapies are currently available for nGD since the recombinant enzymes used in the systemic form of Gaucher disease do not cross the blood-brain barrier. However, a number of promising approaches are currently being tested, including substrate reduction therapy (SRT), in which partial inhibition of the synthesis of the glycosphingolipids (GSLs) that accumulate in nGD lowers their accumulation. We now induce nGD in mice by injection with conduritol B-epoxide (CBE), an irreversible inhibitor of acid beta-glucosidase (GCase), the enzyme defective in nGD, with or without co-injection with GZ-667161, a prototype for SRT. Significant neuropathology, and a reduction in lifespan, was observed upon CBE injection, and this was largely reversed by co-injection with GZ-667161, along with a reduction in glucosylceramide and glucosylsphingosine levels. Analysis of gene expression by RNAseq revealed that GZ-667161 largely reversed the changes in genes and pathways that were differentially-expressed upon CBE injection, specifically pathways of GSL metabolism, lipoproteins and other lipid metabolic pathways, lipid droplets, astrocyte activation, neuronal function, and to some extent, neuroinflammation. Together, this demonstrates the efficacy of SRT to reverse the effects of substrate accumulation on pathological components and pathways in nGD brain.
2020-05-26 | GSE151133 | GEO
Project description:Mannose-specific interactions of Lactobacillus plantarum 299v with jejunal epithelium were investigated using an in situ pig small intestinal segment perfusion (SISP) model. L. plantarum 299v wildtype strain was compared to two isogenic mutant strains either lacking the gene encoding for the mannose-specific adhesin (msa) or sortase (srtA; responsible for anchoring of cell surface proteins like Msa to the cell wall). Salmonella typhimurium served as a positive control for gene expression analysis. Scrapings from jejunal segments were collected after perfusion with bacterial suspensions or PBS (control) for 4 or 8 hours, and host gene expression was assessed using a home-made cDNA porcine microarray. Keywords: host-microbe interaction, Lactobacillus plantarum, mannose-specific adhesion A Small Intestinal Segment Perfusion (SISP) test was performed using 4 pigs. 10 segments were prepared in the jejunum of each pig and perfused with Lactobacillus plantarum 299v wildtype, Lactobacillus plantarum 299v msa mutant strain, Lactobacillus plantarum 299v srtA mutant strain, Salmonella typhimurium or PBS (control) for 4 or 8 hours. Pooled samples from each treatment at each timepoint were used for microarray analysis. 8 comparisons were done: L. plantarum wildtype vs control (4 hours), L. plantarum wildtype vs control (8 hours), L. plantarum msa mutant vs control (4 hours), L. plantarum msa mutant vs control (8 hours), L. plantarum srt mutant vs control (4 hours), L. plantarum srt mutant vs control (8 hours), S. typhimurium vs control (8 hours), samples taken at the beginning of the experiment vs control (8 hours). Dye-swaps were performed for each comparison.
2010-05-25 | E-GEOD-9209 | biostudies-arrayexpress
Project description:The hippocampus contains many unique cell types, which serve the structure’s specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and probe their expression in the SRT data. Using this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.
2024-04-27 | GSE264692 | GEO
Project description:The hippocampus contains many unique cell types, which serve the structure’s specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and probe their expression in the SRT data. Using this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.
2024-04-27 | GSE264624 | GEO
Project description:Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT)
| PRJNA374711 | ENA