EGAS00001001348-sc-2019-06-06T07:57:18Z - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005072 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.
| EGAD00001005073 | EGA
Project description:Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem as well as to multi-site metastases during treatment
| EGAS00001001348 | EGA
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:Accurate analysis of gene expression in human tissues using RNA Sequencing is often dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular, the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lays the foundation for understanding RNA regulation post-mortem, and provide novel insights into RNA metabolism in the tissues of the mammalian eye.
2019-11-04 | GSE135415 | GEO
Project description:Microbiological diagnosis by post-mortem examination
| PRJDB5718 | ENA
Project description:Cellular heterogeneity may bias cell type specific epigenetic patterns leading to a dramatic increase in false positive or negative findings in psychiatric epigenetic studies. To address this issue, we performed fluorescence activated cell sorting (FACS) of neuronal nuclei in post mortem frontal cortex 58 samples followed by Illumina HM450 microarray based DNA methylation profiling. We characterized the extent of neuron and glia specific DNA methylation variation independent of disease status and identified significant cell type specific epigenetic variation at 51% of loci. DNA methylation was profiled for sorted neuronal nuclei from post mortem frontal cortex of 29 major depression and 29 matched control samples using Illumina HM450 microarrays
2013-02-22 | E-GEOD-41826 | biostudies-arrayexpress
Project description:Evaluating RNA quality and transcriptomic profile of beef muscle tissue over time post-mortem may provide insight on RNA degradation and underlying biological and functional mechanisms influencing the biochemical changes occurring post-mortem that transform muscle tissue to meat. RNA-sequencing was performed on longissimus thoracis et lumborum (LTL) muscle samples collected at 5 time points [0 h (45 min post-mortem), 6 h, 24 h, 48 h, and 72 h (drip cooler)] post-mortem from British Continental crossbred beef heifers (n=7). Processed mRNA reads were aligned to the ARS-UCD1.2 bovine genome assembly. Differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend of both up and downregulated genes increasing over time . Gene ontology and KEGG pathway term enrichment analyses revealed significant enrichment of biological and molecular functions relating to cellular energy, oxidative stress and NADH activity specific to early time points, as well as cellular signaling and transport and ribosome activity at specific to late time points. This study also revealed that LTL muscle tissue samples, collected as late as 72 h post-mortem remained at a high RNA integrity, suggesting opportunities for late sampling regimes for RNA-Seq analysis of post-mortem muscle tissue and the potential for larger studies to associate desirable meat quality traits with post-mortem transcriptome activity. Additionally, this study highlights the need to evaluate non-coding genetic features involved with epigenetic regulation in post-mortem muscle tissue, as indicated by non-coding RNA transcripts detected post-mortem, including small nucleolar RNA, mitochondrial DNA genes, and long non-coding RNA.
2021-06-02 | GSE163766 | GEO
Project description:In this study, we evaluated the effects of the post-mortem interval, defined as the number of days elapsed between the death of a donor and the isolation of hCECs, on the properties of hCECs. Using gene profiling, we compared the mRNA profiles of passage 1 hCECs (10 populations) cultivated in moculture with different post-mortem intervals and passage 2 hCECs (6 populations) with different post-mortem intervals from hTECs.
2021-10-08 | GSE185459 | GEO
Project description:Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy. Liver tissue was harvested post-mortem from rats or mice without pregnancy (Nulliparous - NP), time course during pregnancy in days (P2-4, P11-13m P18-20), lactation day 10 (LD10), in during involution of the liver (I2, I4, I6, I8, I10) and 4-weeks regression after preganancy (R4).
2016-12-05 | ST000510 | MetabolomicsWorkbench
Project description:Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy. Liver tissue was harvested post-mortem from rats or mice without pregnancy (Nulliparous - NP), time course during pregnancy in days (P2-4, P11-13m P18-20), lactation day 10 (LD10), in during involution of the liver (I2, I4, I6, I8, I10) and 4-weeks regression after preganancy (R4).
2016-12-04 | ST000509 | MetabolomicsWorkbench