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Sci-Space E14 Mouse Embryo Data

ABSTRACT: Sci-Space E14 Mouse Embryo Data

PROVIDER: PRJNA701618 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13697700_1.fastq.gz	Fastqsanger.gz
	SRR13697700_2.fastq.gz	Fastqsanger.gz
	SRR13697800_1.fastq.gz	Fastqsanger.gz
	SRR13697800_2.fastq.gz	Fastqsanger.gz
	SRR13697900_1.fastq.gz	Fastqsanger.gz

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Sci-Space E14 Mouse Embryo Data

Project description:Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections.

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Project description:More than 2x10E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7x10E6 single nucleotide variant. The database was validated using other two sequencing datasets from other laboratory and high overlap was observed. The identified variant are enriched on intergenic regions, but several thousands reside on gene exons and regulatory regions, such as promoters, enhancers, splicing site and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of this cells. We created a new E14 genome assembly including the new identified variants and used it to map reads from next generation sequencing data generated in our laboratory or in others on E14 cell line. We observed an increase in the number of mapped reads of about 5%. CpG dinucleotide showed the higher variation frequency, probably because of it could be target of DNA methylation. We performed a reduced representation bisulfite sequencing on E14 cell line to test our new genome assembly with respect to the mm9 genome reference. After mapping and methylation status calling, we obtained an increase of about 120,000 called CpG and we avoided about 20,000 wrong CpG calling.

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