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Toxicogenomics data analysis - Basic

Product category: Toxicogenomics
Product code: TGX-DA-B

SciLicium Toxicogenomics services aim at using transcriptomics data to address several challenges in toxicogenomics. After careful planning of exposure conditions, RNA extraction, and library preparation, the toxicogenomics data are pre-processed and used to identify the toxicogenomics signature, to perform functional analysis, and predict and prioritize potential adverse effects.

Basic, Standard, or Advanced, it is up to you to choose and customize the analysis that will suit your project. SciLicium’s experience in toxicogenomics data processing and analysis allows us to offer you various benefits on a wide range of technologies (DNA chips, RNA-seq, single-cell RNA-seq, 5 'or 3' RNA-seq) to screen your compounds.

Basic analysis


You have massive toxicogenomics data and you want to make the best of it without having to worry about the technical aspects or without wasting time on stages such as quality control, data normalization, and basic sample comparisons. SciLicium can take over data preprocessing with standardized and adapted procedures. This critical step will enable you to ensure your samples and sequencing data quality and reliability before starting long and tedious analysis steps. The basic analysis includes three successive steps:


  • Quality control before normalization 
    • Quality of sequencing data 
    • Read distribution across samples
  • Read mapping and gene quantification
    • Read mapping on a reference genome/transcriptome 
    • Transcript/gene quantification 
  • Data normalization: 
    • Data normalization (and standardization) 
    • Batch effect correction (optional)
  • Quality control after normalization 
    • Expression distribution across samples 
    • Number of detected genes 
    • Principal component analysis of samples 
    • Sample correlation


Vendor: SciLicium, Rennes (FRA)



Analysis

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SaferWorldbyDesign integrates in silico and in vitro methods to develop standard and premium Integrated Approaches to Testing and Assessment (IATAs), including methods that support ingredient and formulation screening and testing, product design and the preparation of Regulatory Dossiers.

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Edelweiss Connect GmbH is registered as a limited company with Handelsregisteramt of Kanton Basel-Stadt

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