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Mus musculus strain:C57BL/6

ABSTRACT: E14.5 mouse fetal liver RNA sequencing for multiplexed imaging of nucleome architectures in single cells of mammalian tissue.

PROVIDER: PRJNA622578 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12273002_1.fastq.gz	Fastqsanger.gz
	SRR12273002_2.fastq.gz	Fastqsanger.gz

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Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

Project description:The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. However, how these structures are arranged in the same cell and how they are correlated with each other in different cell types in mammalian tissue are largely unknown. Here, we developed Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We applied this method in mouse fetal liver, and identified de novo cell-type-specific chromatin architectures associated with gene expression, as well as chromatin organization principles independent of cell type. Polymer simulation showed that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our experiments and modeling provide a multiscale and multi-faceted picture of chromatin folding and nucleome architectures in mammalian tissue and illustrate physical principles for maintaining chromatin organization. Here we submit our bulk RNA-sequencing data on E14.5 mouse fetal liver, used in the study to validate image-based RNA profiling results.

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Project description:This study analyzes gene expression in beta-thalassemic fetal liver erythroblasts in the Th3 murine model. FACS-purified wild-type, heterozygous, and homozygous stage-matched erythroblasts from E14.5 fetal livers are compared. We used FACS to purify CD71+Ter119+FSChigh matched populations from E14.5 fetal livers of wild-type, Th3/+, and Th3/Th3 embryos

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