Ontology highlight
ABSTRACT:
PROVIDER: PRJNA877080 | ENA |
REPOSITORIES: ENA
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Project description:Oudekraal long term monitoring project
| PRJEB50389 | ENA
Project description:As part of the ENCODE consortium project (NIH, NHGRI), we conducted genome-wide location analysis for various transcription factors in various cell types. The long-term goal of this project is to determine the function of each DNA nucleotide in the genome. Measurement of transcription factor binding events is an important part of this effort. Here we measure genome-wide binding events for a variety of important transcriptional regulators. Keywords: ChIP-chip
2007-07-19 | GSE8489 | GEO
Project description:Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. Given their functional and clinical relevance, small EVs have emerged as a promising target among the liquid biopsy approaches for cancer detection. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive. In this study, we established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC). By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitundial cohorts, we uncovered 28 EV-miRs for detecting mCRC, and 131 EV-miRs for long-term monitoring of tumor size progression. Among these candidates, we further pinpointed a 15-EV-miR signature with dual detection and monitoring functions for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker – aside from its diagnostic power, its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Furthermore, target spectrum of this 15-EV-miR signature of mCRC suggested an involvement of small EVs in programming the mesenchymal–epithelial transition (MET) transition for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche. Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in tumor therapeutic monitoring.
2022-09-14 | GSE188627 | GEO
Project description:Given the association between mutational load and cancer, the observation that genetic aberrations are frequently found in human pluripotent stem cells (hPSCs) is of concern. Prior studies in hiPSCs have shown that deletions and regions of loss-of-heterozygosity (LOH) tend to arise during reprogramming and early culture, while duplications more frequently occur during long-term culture. For the corresponding experiments in hESCs, we studied two sets of hESC lines: one including the corresponding parental DNA; and the other generated from single blastomeres from four sibling embryos. Here, we show for the first time that genetic aberrations observed in hESCs can originate during preimplantation embryo development and/or early derivation. These early aberrations are mainly deletions and LOH, while aberrations arising during long-term culture of hESCs are more frequently duplications. Our results highlight the importance of close monitoring of genomic integrity and the development of improved methods for derivation and culture of hPSCs.
2014-04-21 | GSE49452 | GEO
Project description:Brief description of the data submitted: Three LC-MS/MS files acquired using Data Dependent Acquisition (DDA) for
(1) NIST 1950 Frozen Human Plasma standard reference material subjected to reversed-phase chromatographic (RPC) metabolomic assay tailored for complex lipid separation;
(2) plasma Long-Term Reference (LTR) sample, routinely integrated in profiling studies at the National Phenome Centre for study-independent monitoring of precision, analysed by hydrophilic interaction liquid chromatography (HILIC) metabolomic assay tailored for small molecule polar metabolites;
(3) pooled Long-Term Reference (LTR) urine sample, routinely integrated in profiling studies at the National Phenome Centre for study-independent monitoring of precision, analysed by reversed-phase chromatographic (RPC) metabolomic assay tailored for small molecule metabolites.
Paper title: MS2Query: Reliable and Scalable MS2 Mass Spectral-based Analogue Search
Author list: Niek F. de Jonge, Joris R. Louwen, Elena Chekmeneva, Stephane Camuzeaux, Femke J. Vermeir, Robert S. Jansen, Florian Huber, Justin J.J. van der Hooft
Citation: bioRxiv 2022.07.22.501125; doi: https://doi.org/10.1101/2022.07.22.501125
2022-11-04 | MSV000090642 | MassIVE