Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1171828 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30954241_1.fastq.gz | Fastqsanger.gz | |||
| SRR30954241_2.fastq.gz | Fastqsanger.gz | |||
| SRR30954242_1.fastq.gz | Fastqsanger.gz | |||
| SRR30954242_2.fastq.gz | Fastqsanger.gz | |||
| SRR30954243_1.fastq.gz | Fastqsanger.gz |
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Project description:The post-mortem interval (PMI) is the time that elapses since the death of an individual until the body is found. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI, since they can better support degradation. To find potential biomarkers for PMI estimation, we analyzed the miRNome at early PMI in rat skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 micoarrays. In this dataset, we include the expression of 1218 rat miRNAs at early postmortem interval.
2023-01-02 | GSE208236 | GEO
Project description:Transcription profiling of human post-mortem brain tissue (orbitofrontal cortex) from patients with bipolar disorder and matched healthy controls
2025-01-24 | E-GEOD-5389 | ExpressionAtlas
Project description:Methods currently available to estimate the post-mortem submerged interval (PMSI) of cadavers in water suffer from poor accuracy, being mostly based on morphological examination of the remains. Proteins present within bones have recently attracted more attention from researchers interested in the estimation of the post-mortem interval (PMI) in terrestrial environments. Despite the great potential of proteomic methods for PMI estimation, their application to aquatic environments has not yet been explored. In this study, we examined whether four different types of aquatic environment (tap water, saltwater, pond water and chlorinated water) affected the proteome of mice bones with increasing PMSIs (from zero to three weeks).
2020-04-06 | PXD017386 | Pride
Project description:Fresh frozen post mortem prefrontal cortex tissue (Brodman area 46) was obtained from 44 individuals varying in age from 0 to 49 years. RNA was extracted from these samples and hybridized to HG133plus2.0 GeneChips. The data was used to examine patterns of gene expression over the course of human postnatal developmental and ageing. PMI - postmortem interval, DLPFC - dorsolateral prefrontal cortex
2009-11-11 | GSE13564 | GEO
Project description:Recent developments in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)-based proteomics have drastically increased analytical depth and sample throughput, establishing a robust tool for comprehensive system-wide analyses. Such analyses are instrumental in studying the pathophysiology of diseases. One crucial source of material for this is post-mortem individuals. However, there is a significant gap in our understanding of the multi-organ temporal impacts of body decomposition on the proteome. This deficiency compromises result validity due to challenges in controlling the post-mortem interval (PMI). To address this, we reanalyzed published data to compare the effect of the PMI on the proteome alterations to the disease effects. Additionally, we conducted a clinically relevant time-course experiment using isogenic mice and applied LC-MS/MS in data-independent acquisition (DIA) mode to systematically study the proteome alterations post-mortem. Our experiment uncovered dramatic organ-specific protein regulation post-mortem, with only certain aspects attributable to protein autolysis suggesting active post-mortem protein regulation. Notably, the liver and spleen exhibited substantial proteome changes within hours of PMI, while the heart showed comparatively modest changes even after 96 hours. Subcellular fractionation of the heart led to an unexpected surge in the number of proteins exhibiting abundance differences early in PMI. We conducted a compressive analysis of semi-tryptic peptides for the first time, revealing distinct consensus motifs for different organs, indicating organ-specific protease activity. In conclusion, when designing LC-MS/MS-based studies, meticulous consideration of sample collection is crucial as PMI effects may outweigh disease effects. It is preferred that both experimental and control samples are taken in the operation room, especially for studies including subcellular fractionation or trans-organ comparison. In single-organ studies, the planning should involve careful control of the PMI, preferably by sample matching.
2024-12-17 | PXD053048 | Pride
Project description:The estimation of the post-mortem interval (PMI) and the age-at-death (AAD) are crucial steps in the medico-legal investigation of unidentified human remains. Current methods to estimate PMI and AAD suffer from a lack of accuracy and objectivity, particularly when the remains are in an advanced state of decomposition. Recently, proteomics studies using animal models have identified potential biomarkers for PMI and AAD estimation. This study investigated the human bone proteome in four human body donors studied throughout decomposition outdoors. We compared different bone tissues (tibia and iliac crest) from body donors of known AAD, and compared bone samples taken shortly after death to bone samples upon complete skeletonization of the body. The effects of ageing phenomena (in vivo and post-mortem) and the surrounding environment on the variability and abundancy of the bone proteome were assessed.
2021-09-09 | PXD019693 | Pride
Project description:Fresh frozen post mortem prefrontal cortex tissue (Brodman area 46) was obtained from 44 individuals varying in age from 0 to 49 years. RNA was extracted from these samples and hybridized to HG133plus2.0 GeneChips. The data was used to examine patterns of gene expression over the course of human postnatal developmental and ageing. PMI - postmortem interval, DLPFC - dorsolateral prefrontal cortex Experiment Overall Design: The dataset consists of 44 individuals varying in age from 0 to 49 years
2009-12-02 | E-GEOD-13564 | biostudies-arrayexpress
Project description:Introduction: The analysis of post-mortem metabolomic changes in biological fluids opens the way to develop new methods for the estimation of post-mortem interval (PMI). It may also help in the analysis of disease-induced metabolomic changes in human tissues when the postoperational samples are compared to the post-mortem samples from healthy donors. Objectives: The goals of this study are to observe and classify the post-mortem changes occurring in the rabbit blood, aqueous and vitreous humors (AH and VH), to identify the potential PMI markers among a wide range of metabolites, and also to determine which biological fluid – blood, AH or VH – is more suitable for the PMI estimation. Methods: The quantitative metabolomic profiling of samples of the rabbit serum, AH and VH taken at different PMIs has been performed with the combined use of high-frequency NMR and high-resolution LC-MS methods. Results: The quantitative levels of 63 metabolites in the rabbit serum, AH and VH at different PMIs have been measured. It has been found that the post-mortem metabolomic changes in AH and VH proceed slower than in blood, and the data scattering is lower. Among the metabolites whose concentrations increase with time, the most significant and linear growth is found for hypoxanthine, choline and glycerol. Conclusion: The obtained results indicate the advantage of ocular fluids, AH and VH, over blood serum for the search of potential biochemical markers for the PMI estimation. Among the compounds studied in the present work, hypoxanthine, choline and glycerol give the biggest promise as the potential PMI biomarkers.
2017-08-23 | MTBLS349 | MetaboLights
Project description:In other analysis in the current manuscript, we find a similar gene signature (to dissociation based artifacts in mouse and human tissue) is present in post-mortem microglia and astrocytes, across all snRNA-seq datasets analyzed, although it is highly variable between subjects. ​
Using acutely-resected neurosurgical tissue, we performed single-nucleus RNA-seq and reveal that a similar signature can be detected in microglia following prolonged exposure to room temperature. Tissue handling and methods details, as well as sequencing and analysis details) can be found in the methods section of related manuscript (Marsh et al., 2022).
Together, these results suggest that the presence of this signature in post-mortem brain samples may be the result of a combination of acute pre-mortem (agonal state, cause of death, comorbidities, etc.) and post-mortem (post-mortem interval (PMI), storage time, RNA quality, etc.) variables and may not represent normally present cell state.
| EGAD00001008541 | EGA
Project description:Recent studies suggest that genetic and environmental factors do not account for all the schizophrenia risk and epigenetics also plays a role in disease susceptibility. DNA methylation is a heritable epigenetic modification that can regulate gene expression. Genome-Wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485 000 CpG sites using the Illumina Infinium Human Methylation450 Bead Chip. After adjusting for age and post-mortem interval (PMI), 4 641 probes corresponding to 2 929 unique genes were found to be differentially methylated. Of those genes, 1 291 were located in a CpG island and 817 were in a promoter region. These include NOS1, AKT1, DTNBP1, DNMT1, PPP3CC and SOX10 which have previously been associated with schizophrenia. More than 100 of these genes overlap with a previous DNA methylation study of peripheral blood from schizophrenia patients in which 27 000 CpG sites were analysed. Unsupervised clustering analysis of the top 3 000 most variable probes revealed two distinct groups with significantly more people with schizophrenia in cluster one compared to controls (p = 1.74x10-4). The first cluster was composed of 88% of patients with schizophrenia and only 12% controls while the second cluster was composed of 27% of patients with schizophrenia and 73% controls. These results strongly suggest that differential DNA methylation is important in schizophrenia etiology and add support for the use of DNA methylation profiles as a future prognostic indicator of schizophrenia Genome-Wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485 000 CpG sites using the Illumina Infinium Human Methylation450 Bead Chip.
2014-09-05 | E-GEOD-61107 | biostudies-arrayexpress