Fb66fd1d-9d8c-4f33-a55d-baf9a57ba582 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006936 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Little is known of the geospatial architecture of individual cell populations in lung adenocarcinoma (LUAD) evolution. Here, we perform single-cell RNA sequencing as well as single-cell BCR sequencing of cells from 16 LUADs and 47 multi-region normal lung tissues of defined spatial proximities from the tumors. Our multi-region single-cell sequencing analyses unravel cell populations, states, and phenotypes in the spatial and ecological evolution LUAD from the lung that comprise high-potential targets for early interception.
| EGAS00001005021 | EGA
Project description:Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.
2020-09-16 | GSE137986 | GEO
Project description:Deciphering the complexity of non-small cell lung cancer (NSCLC) evolutionary histories may elucidate the basis for its dismal outcome. We performed multi-region sequencing on 25 regions from seven early-stage NSCLCs. Spatial dissection revealed branched tumor evolution, with driver mutations occurring before and after subclonal diversification. Intra-tumor heterogeneity in DNA copy number alterations, translocations and endogenous APOBEC mutational processes, demonstrates that NSCLC may follow multiple distinct evolutionary trajectories simultaneously. In smokers, despite maintained carcinogen exposure, temporal dissection reveals a proportional decrease in smoking-related mutations during tumor progression, accompanied by an increase in APOBEC-related mutations. We observed genome-doubling events early in tumor development of ex-smokers, suggesting prolonged latency periods before clinical detection. Multi-region sequencing demonstrates the relentless and heterogeneous nature of genomic instability processes in early-stage NSCLCs.
| EGAS00001000840 | EGA
Project description:Deciphering the complexity of non-small cell lung cancer (NSCLC) evolutionary histories may elucidate the basis for its dismal outcome. We performed multi-region sequencing of early-stage NSCLCs. Spatial dissection revealed branched tumor evolution, with driver mutations occurring before and after subclonal diversification. Intra-tumor heterogeneity in DNA copy number alterations, translocations and endogenous APOBEC mutational processes demonstrates that NSCLC may follow multiple distinct evolutionary trajectories simultaneously. In smokers, despite maintained carcinogen exposure, temporal dissection reveals a relative decrease in smoking-related mutations during tumor progression, accompanied by an increase in APOBEC-related mutations. In the tumors from ex-smokers, genome-doubling occurred before subclonal diversification, suggesting prolonged latency before clinical detection. Multi-region sequencing demonstrates the relentless and heterogeneous nature of genomic instability processes in early-stage NSCLCs.
| EGAS00001000809 | EGA
Project description:Purpose Gallbladder cancer (GBC) is a highly malignant tumor with extremely poor prognosis. Previous studies have suggested that the carcinogenesis and progression of GBC is a multi-stage and multi-step process, but most of them focused on the genome changes. And a few studies just compared the transcriptome differences between tumor tissues and adjacent noncancerous tissues. The transcriptome changes, relating to every stage of GBC evolution, have rarely been studied. Methods We selected three cases of normal gallbladder, four cases of gallbladder with chronic inflammation induced by gallstones, five cases of early GBC, and five cases of advanced GBC, using next-generation RNA sequencing to reveal the changes in mRNAs and lncRNAs expression during the evolution of GBC. Results In-depth analysis of the sequencing data indicated that transcriptome changes from normal gallbladder to gallbladder with chronic inflammation were distinctly related to inflammation, lipid metabolism, and sex hormone metabolism; transcriptome changes from gallbladder with chronic inflammation to early GBC were distinctly related to immune activities and connection between cells; and the transcriptome changes from early GBC to advanced GBC were distinctly related to transmembrane transport of substances and migration of cells. Conclusion Expression profiles of mRNAs and lncRNAs change significantly during the evolution of GBC, in which lipid-based metabolic abnormalities play an important promotive role, inflammation and immune activities play a key role, and changes in membrane proteins are the most highlighted molecular changes.
2022-05-31 | GSE202479 | GEO
Project description:Untargeted metabolomics analyses were performed on clinically matched baseline plasma samples (n = 16 per group) prospectively collected from patients with clinically low-risk early stage prostate cancer undergoing AS who exhibited early disease progression (DP) (defined as upgrading of Gleason score (GS) and/or increased tumor volume on surveillance biopsy within 18 months after start of AS) or indolent disease (no progression for five or more years after start of AS) as well as 459 baseline plasma samples prospectively collected from patients with early-stage prostate cancer undergoing AS.
2020-05-19 | ST001408 | MetabolomicsWorkbench
Project description:Sample-matched multi-omic measurements of fourteen virulence-essential regulator mutants were coupled with computational network analysis to efficiently identify Salmonella virulence factors. A subset of computationally predicted virulence factors was determined to be secreted into the host cytoplasm, and two of these, SrfN and PagK2, were required for full mouse virulence and defined a new class of translocated effectors involved in pathogenesis.
2013-10-07 | PXD000390 | Pride
Project description:Multi-region Illumina whole-exome and/or whole-genome sequencing on tumor regions collected from early-stage NSCLC patients who underwent definitive surgical resection prior to receiving adjuvant therapy.
Patients covered by this dataset: L012, L013, L015, L017
| EGAD00001001918 | EGA
Project description:The salt glands in the epidermis of recretohalophytes play a pivotal role in salt tolerance by secreting excess salts from tissues. Irrespective of the importance of understanding the secretion process, nothing is known about the molecular mechanisms of salt gland development. Limonium bicolor possesses multi-cellular salt glands in the epidermis and provides a model to study salt gland development. We applied next-generation sequencing to profile early leaf development using five distinctly different developmental stages, which were quantified by successive collections of the first true leaf of L. bicolor with precise spatial and temporal resolution. Twenty-two percent of the genes were differentially expressed along the developmental gradient. Cluster analysis revealed specific expression patterns at one stage, and identified enriched functions specific for each developmental stage. Seventy-two genes were identified as highly involved in salt gland differentiation. Salt glands have high homology with trichomes, which was also confirmed by mutants with increased salt gland densities. A model is proposed to illustrate genes participating in salt gland differentiation. This unique dataset lays the foundation for identifying key genes involved in salt gland development and salt secretion, which is a requisite for understanding mechanisms that could make agriculture possible in saline areas worldwide.
2016-11-18 | GSE52549 | GEO
Project description:To illuminate the evolutionary trajectory of LUAD from AIS to IAC, high-throughput scRNA-seq and ST data were generated and integrated to create a large-scale, single-cell spatiotemporal atlas of LUAD. We compiled a multi-omics atlas of the early-stage LUAD invasion process that reflects the heterogeneity of cancer cells, the competitive polyclonal origin of LUAD, signalling interactions between cancer cells and the TME, and the pseudo-chronological nature of LUAD invasion. The spatial distribution characteristics of LUAD cells revealed the spatial heterogeneity of LUAD and the mechanism of spatial immune escape in LUAD, which provides strong evidence supporting clinical diagnosis and surgical intervention at the single-cell level.
2021-11-30 | GSE189357 | GEO