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Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [Hi-C]

ABSTRACT: Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [Hi-C]

PROVIDER: PRJNA1103723 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28780120_1.fastq.gz	Fastqsanger.gz
	SRR28780120_2.fastq.gz	Fastqsanger.gz

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Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [Hi-C]

Project description:Molecular and cellular characterization of tumors has become essential due to the complex and heterogeneous nature of cancer disease. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a challenge for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows recovery of highly viable cell suspensions from breast cancer biopsies. Using these cell suspensions we successfully characterized genome architecture through Hi-C. Also, we evaluated single-cell gene expression and the tumor cellular microenvironment through single cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here opens the possibility to obtain viable cell suspensions from biopsies in a simple and efficient manner

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Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq1]

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Project description:Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq1]

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Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq 2]

Project description:Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq 2]

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Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis

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Project description:Coffee is one of the most important commodities cultivated worldwide and has great economic impact in producing countries. Although 130 different species belonging to the coffea gender have been described, only two of them are commercially exploited: Coffea arabica and Coffea canephora. C. arabica is responsible for 61% of the world production (Van der Vossen et al., 2015). However, due to the narrow genetic back ground, classical genetic breeding is time consuming and takes around 30 years (Santana-Buzzy et al., 2007; Hendre et al., 2014). Several genetic engineering and biotechnological tools have been successfully applied in coffee breeding. Somatic embryogenesis (SE) is a process in which new viable embryos are produced from somatic tissues. It is one of the most promising production processes (Santana-Buzzy et al, 2007; Marsoni et al., 2008). A better understanding of the molecular basis related to somatic embryogenesis will give insight into the process of embryo formation and totipotency and will allow the development of new in vitro culture strategies for the propagation and genetic manipulation of elite cultivars (Marsoni et al., 2008). High throughput proteomics in coffee is limited so far to 2D gel based proteomics techniques. Although really useful and the most common technique for plants, 2DE is limited in throughput and a gel free technique allow to go a step further (Carpentier & America, 2014; Vanhove et al., 2015). To improve the knowledge about somatic embryogenesis, we present the first high throughput proteome profile (1051 confident protein identifications) of coffee embryogenic cell suspensions developed from leaves of Coffea arabica cultivar Catuaí.

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