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Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

ABSTRACT: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

PROVIDER: PRJNA659788 | ENA |

REPOSITORIES: ENA

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			Action	DRS
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	SRR12551286_1.fastq.gz	Fastqsanger.gz
	SRR12551286_2.fastq.gz	Fastqsanger.gz
	SRR12551288_1.fastq.gz	Fastqsanger.gz
	SRR12551288_2.fastq.gz	Fastqsanger.gz

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Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

Project description:Recently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. elegans is a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the Latent Dirichlet Allocation algorithm, our chromatin accessibility data provide new insights into which genomic loci may be participating in cell type-specific gene regulation, with promise for better understanding of cellular differentiation and gene regulation in the worm.

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Comprehensive characterization of tissue-specific chromatin accessibility in L2 <i>Caenorhabditis elegans</i> nematodes.

Project description:Recently developed single-cell technologies allow researchers to characterize cell states at ever greater resolution and scale. Caenorhabditis elegans is a particularly tractable system for studying development, and recent single-cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns give insight about gene function and into the biochemical state of different cell types; recent advances in other single-cell genomics technologies can now also characterize the regulatory context of the genome that gives rise to these gene expression levels at a single-cell resolution. To explore the regulatory DNA of individual cell types in C. elegans, we collected single-cell chromatin accessibility data using the sci-ATAC-seq assay in L2 larvae to match the available single-cell RNA-seq data set. By using a novel implementation of the latent Dirichlet allocation algorithm, we identify 37 clusters of cells that correspond to different cell types in the worm, providing new maps of putative cell type-specific gene regulatory sites, with promise for better understanding of cellular differentiation and gene regulation.

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