Curated Public Data
NEBION curates and integrates high quality omics datasets from various public repositories and collections. The entire compendium of NEBION curated data is fully consistent regarding format, vocabularies used, and data processing. Improvements in formats or vocabularies are implemented retrospectively on all existing data.
Repositories : GEO, ArrayExpress, SERA, dbGAP, etc.
Collections : TCGA, CCLE, Drug Matrix, CMAP, LINCSS, etc.
The focus of this curation is on pharmaceutical and biotech companies, nutrition and cosmetics, and also applied and fundamental academic research. Over 200,000 samples (microarrays, RNA-seq) have already been quality controlled, standardized and precisely described (annotated), providing a coverage of over 500 tissue/cell types, 1500 cell lines, 700 cancer types, and over 15,000 experimental conditions.
– Oncology and hematology
– Immunology and rheumatology
– Respiratory diseases
– Cardiovascular diseases
– Endocrinology and metabolism
– Neurodegenerative diseases
– Pharmacology and toxicology
For over 10 years, the NEBION plant curation team has assembled, curated and integrated data from a wide variety of experimental contexts and species.
– Model plants: Arabidopsis and Medicago
– Monocot crops: Maize, rice, wheat, barley, sorghum
– Dicot crops: Soybean, tomato, tobacco
– Organs, tissues and cell types
– Genotypes and knock-outs
– Chemical and hormonal treatments
– Biotic and abiotic stresses
– Hormonal treatments
– Stages of development
– Circadian rythm
At present curated data is available for the two model species Escherichia coli and Saccharomyces cerevisiae.
– Cell cycle studies
– Culture conditions
– Knock-out lines