Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The second sequencing batch

ABSTRACT: The second sequencing batch

TISSUE(S): ['oral Cavity', 'pharynx', 'gut', 'urine']

SUBMITTER: Chenfen Zhou

PROVIDER: OEX00021105 | NODE | 2022-11-23

REPOSITORIES: NODE

ACCESS DATA

Json Xml

Similar Datasets

Nassar2022 - Microbiome sequencing NER model

Project description:Microbiome sequencing model is a Named Entity Recognition (NER) model that identifies and annotates microbiome nucleic acid sequencing method or platform in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with sequencing metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications

2022-02-21 | MODEL2202170012 | BioModels

Next Generation Protein Sequencing

Project description:NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysis, de-novo long peptide tag sequencing of resulting peptides and assembly of peptide tags into consensus contigs.

2017-04-03 | PXD003804 | Pride

The combination human 13 gene mutation Detection kit (reversible terminal termination sequencing) complements the clinical trial

Project description:Interventions: Gold Standard:Comparison methods :(1) comparison of similar kits;(2) Sequencing method;Index test:Human 13 gene mutation Combination Detection Kit (reversible terminal termination sequencing method) Primary outcome(s): Lung and gastrointestinal tumor genes Study Design: Sequential

| 2696826 | ecrin-mdr-crc

GNPS ASM 2017 ili Demo Sequencing and Metabolomics Data

Project description:.stl file and 16S sequencing (deblurred) OTU table and metabolomics table with xyz coordinates

2017-05-23 | MSV000081106 | GNPS

Crotonylomics sequencing of human colon cancer cell lines

Project description:P53 mutation is closely associated with the occurrence and progression of colon cancer. In this project, we did crotonylomics sequencing by using human colon cancer homologous cell line pair-HCT116+/+(with wild type p53) and HCT116-/- (with null p53). Crotonylomics sequencing results showed that p53 deficiency regulated crotonylation of non-histone proteins.

2024-05-22 | PXD047258 | Pride

Clinical trials verifying the consistency of AmoyDx Essential NGS Panel (Reversible Terminator Sequencing) with local tests

Project description:Interventions: Gold Standard:Histopathological diagnosis;Index test:AmoyDx Essential NGS Panel (Reversible Terminator Sequencing) Primary outcome(s): EGFR 20 insertion mutation;consistency Study Design: Factorial

| 2699936 | ecrin-mdr-crc

Integrated with Proteome-sequencing, bulk RNA-sequencing and Single cell RNA-sequencing to identify potential biomarkers in different grades of intervertebral disc degeneration

Project description:We selected humann intervertebral disc samples to perform proteomics analysis. There were 1 case of grade I , 1 case of grade II, 3 cases of grade Ⅲ and 3 cases of grade Ⅳ according to Pfirrmann classfication. RNA seqencing analysis and single-cell RNA sequencing were integrated with proteomics data to identify the hub genes for intervertebral disc degeneration using bioinformatic method.

2023-05-10 | PXD040593 | Pride

De novo sequencing of DIA data

Project description:Testing datasets and pre-trained model for DeepNovo, a deep learning-based tool for de novo sequencing of DIA data.

2018-05-16 | MSV000082368 | MassIVE

Application of de novo sequencing to large-scale complex proteomics datasets

Project description:Dependent on concise, pre-defined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large scale proteomics datasets, and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) which leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches.

2016-01-12 | PXD003317 | Pride

Open, multicentre study for the diagnosis of Lynch syndrome using foss sequencing platform in colorectal cancer patients with immunohistochemical indications of MMR protein deficiency

Project description:Interventions: Gold Standard:Pathological examination;Index test:New Caicon Panel Primary outcome(s): New caicon panel sequencing Study Design: Sequential

| 2688576 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data