Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Studying heterogeneity in embryonic stem cells using the approach of search-engine

ABSTRACT: Studying heterogeneity in embryonic stem cells using the approach of search-engine

PROVIDER: PRJNA792553 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Studying heterogeneity in embryonic stem cells using the approach of search-engine

Project description:Here we designed a search-engine for single-cell epigenome profiles. We tested different application of search-engine using different data-sets including mESC scATAC-seq profile.

2022-12-27 | GSE192644 | GEO

Studying the genetic heterogeneity in mouse dopamine neurons

Project description:Studying the genetic heterogeneity in mouse dopamine neurons

| PRJNA473654 | ENA

Search Engine for Antimicrobial Resistance

Project description:Search Engine for Antimicrobial Resistance: a cloud compatible pipeline and web interface for rapidly detecting antimicrobial resistance genes directly from sequence data

| PRJEB4647 | ENA

GlycoNote search engine

Project description:Mass spectrometry is a central technique in glycomic analysis. However, there is no generic software tool for automated, confident analysis of tandem-mass spectrometry based glycomic data. Here, we propose GlycoNote – a generic and reliable search engine for tandem-mass spectrometry based glycomics. A false discovery rate analysis based on iterative decoy searching was specifically designed for glycomic data analysis. We apply GlycoNote to the analyses of distinct glycomic samples, including human milk oligosaccharides, N/O-glycome from human cell line and polysaccharides from plant. To further demonstrate the general utility of GlycoNote, automated analyses of nonnative glycomes (N-glycome labeled with aniline and permethylated N-glycome) or atypical glycans (O-glycome with N-acetylneuraminic acid / N-glycome from C. elegans) were performed. More importantly, an open-search mode was introduced for the elucidation of component heterogeneity in samples. GlycoNote could be an important tool in the rapidly growing efforts toward comprehensive glycomic analysis.

2019-07-23 | PXD014705 |

MS Annika: A new Cross-Linking Search Engine

Project description:A cross linking mass spectrometry search engine was developed and implemented into Thermo Proteome Discoverer. The search engine is capable to handle several linker types as well as data input formats. To demonstrate its ability processing Bruker -ion mobility data, synthetic peptides (Beveridge, et. al., Nat. Commun., 2020, doi: 10.1038/s41467-020-14608-2) were analyzed and the respective files are availible here.

2021-05-27 | PXD022772 | Pride

Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach

Project description:Variable tumor cellularity can limit sensitivity and precision in comparative genomics, because differences in tumor content can result in misclassifying truncal mutations as region-specific private mutations in stroma-rich regions, especially when studying tissue specimens of mediocre tumor cellularity such as LUADs. To address this issue, we refined a nuclei flow-sorting approach by sorting nuclei based on ploidy and the LUAD lineage marker thyroid transcription factor 1 (TTF-1) and applied this method to investigate genome-wide somatic copy number aberrations (SCNA) and mutations of 409 cancer genes in 39 tumor populations obtained from 16 primary tumors and 21 matched metastases. This approach increased the mean tumor purity from 54% (range: 7-89%) of unsorted material to 92% (range: 79-99%) after sorting. Despite this rise in tumor purity, we detected limited genetic heterogeneity between primary tumors and their metastases. In fact, 88% of SCNAs and 80% of mutations were propagated from primary tumors to metastases and low allele frequency mutations accounted for much of the mutational heterogeneity. Even though the presence of SCNAs indicated a history of chromosomal instability (CIN) in all tumors, metastases did not have more SCNAs than primary tumors. Moreover, tumors with biallelic TP53 or ATM mutations had high numbers of SCNAs, yet they were associated with a low interlesional genetic heterogeneity. The results of our study thus provide evidence that most macroevolutionary events occur in primary tumors before metastatic dissemination and advocate for a limited degree of CIN over time and space in this cohort of LUADs. Sampling of primary tumors thus may suffice to detect most mutations and SCNAs. In addition, metastases but not primary tumors had seeded additional metastases in three of four patients; this provides a genomic rational for surgical treatment of such oligometastatic LUADs.

2018-09-11 | GSE119763 | GEO

D-score - D-score: a search engine independent MD-score

Project description:Processing of the dataset of synthetic phosphopeptides by Savitzki et al. (MCP, 2011) using multiple search engines. Establishment of the D-score: a search engine independent MD-score.

2013-01-23 | PXD000021 | Pride

SEARCH ProDIGY Exome Sequencing Study

Project description:SEARCH ProDIGY Exome Sequencing Study

| PRJNA422645 | ENA

SEARCH ProDIGY Exome Sequencing Study

Project description:SEARCH ProDIGY Exome Sequencing Study

| PRJNA422646 | ENA

MERFISH reveals embryonic endothelial heterogeneity

Project description:MERFISH reveals embryonic endothelial heterogeneity

| PRJNA1038713 | ENA