Dissociation for single-cell RNA-seq

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Table of contents

I INTRODUCTION 
Toxicology: a useful tool for evaluate the risk assessment in the cosmetic industry
1.1 The cosmetic industry
The Respiratory Tract 
2.1 Upper airways
2.1.1 Nose and the nasal cavities
2.1.2 Paranasal sinuses
2.1.3 Pharynx
2.1.4 Larynx
2.2 Lower respiratory tract
2.2.1 Trachea
2.2.2 Bronchi and bronchioles
2.2.3 Alveoli
2.3 The airway epithelium cell composition
2.3.1 Basal cells
2.3.2 Suprabasal cells
2.3.3 Secretory cells.
2.3.4 Multiciliated cells
2.3.5 Rare cells
Toxicity of Inhaled toxicants 
3.1 Deposition of inhaled toxicants in the respiratory tract
3.2 The respiratory tract protective mechanisms
3.3 Lung cancer
3.3.1 The cellular origins of lung cancer
Chemicals risk assessments 
4.1 Standard toxicity tests for risk assessmen
4.2 In vitro models
4.3 Adverse outcome pathway
The Toxicogenomics 
5.1 Transcriptomics
5.2 Proteomics
5.3 Metabolomics
5.4 Epigenomics
Single cell RNA sequencing: a powerful tool for the toxicogenomics 
6.1 Single cell RNA sequencing
6.2 Single cell study: from bench to bioinformatic analysis
6.3 Tissue dissociation
6.4 Cell isolation
6.5 Unique Molecule Identifier (UMI)
6.6 Single cell sequencing protocols: the droplet based approach
6.7 Statistical data analysis
6.8 Different applications for single-cell transcriptomic approach
6.8.1 Possible applications in the medical field
6.8.2 Single-cell in developmental biology
6.8.3 Cell atlases
6.8.4 Toxicology at single-cell resolution
II MATERIAL AND METHODS 
7.1 Cell lines and reagents
7.2 RNA extraction
7.3 Quantitative RT-PCR
7.4 Microarry gene expression analysis
7.5 Dissociation for single-cell RNA-seq
7.6 Single-cell RNA-seq
III RESULTS 
Research context and aims 
8.1 Non-genotoxic carcinogenic compounds
8.1.1 Cadmium chloride
8.1.2 Hydroquinone
8.1.3 Phorbol 12-myristate 13-acetate
8.2 Aim of the project
Experimental findings 
9.1 Setting up the experimental conditions
9.2 Bulk transcriptomic approach: Microarray gene expression analysis
9.3 Setting up the single cell RNA sequencing experiment
9.4 Single-cell RNA sequencing analysis
9.4.1 Presentation of the datasets
9.4.2 BEAS-2B and cell subtype
9.4.3 Hierarchy of cell response
9.4.4 Common signature
9.4.5 Specific signature
IV DISCUSSION 
10.3 Towards the elaboration of an in vitro test using transcriptomic approaches
10.3.1 Experimental conditions
10.3.2 The models under the lens of the microarray gene expression analysis
10.3.3 The contribution of the scRNA-seq analysis
10.3.4 What are BEAS-2B cells in relation to cell-types present in the MucilAirTM ALI culture?
10.3.5 A hierarchy in cell response in MucilAirTM ALI culture
10.3.6 A common signature to all cell types
10.3.7 A specific signature to all cell types
V CONCLUSION AND PERSPECTIVES 
VI ANNEXES 
11.1 A Role for metformin in the treatment of Dupuytren disease? 
11.1.1 Dupuytren Disease
11.1.2 Carpal Tunnel Syndrome
11.1.3 Metformin
11.1.4 Scientific article
11.2 Blockade of pro-fibrotic response mediated by the miR-143/145 cluster prevents targeted therapy-induced phenotypic plasticity and resistance in melanoma
11.3 Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics
VI BIBLIOGRAPHY