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Accession: PRJNA765363 ID: 765363

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. More...
AccessionPRJNA765363; GEO: GSE184554
TypeUmbrella project
PublicationsBonora G et al., "Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.", Genome Biol, 2021 Sep 27;22(1):279
SubmissionRegistration date: 21-Sep-2021
4D Nucleome - Data Coordination and Integration Center
RelevanceSuperseries
Project Data:
Resource NameNumber
of Links
Sequence data
SRA Experiments25
Publications
PubMed1
PMC1
Other datasets
BioSample16
GEO DataSets4
GEO Data Details
ParameterValue
Data volume, Supplementary Mbytes462
SRA Data Details
ParameterValue
Data volume, Gbases793
Data volume, Tbytes0.41
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation encompasses the following 3 sub-projects:
Project TypeNumber of Projects
Epigenomics1
BioProject
accession
OrganismTitle
PRJNA765361Mus musculus4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body (4D Nucleome - Data Coordination...)
Other1
BioProject
accession
OrganismTitle
PRJNA770075Mus musculus4DNESB7XYI9V - sci-Hi-C on mESCs differentiated to embryoid body (4D Nucleome - Data Coordination...)
Transcriptome or Gene expression1
BioProject
accession
OrganismTitle
PRJNA765362Mus musculus4DNESCX7WHJ1 - sci-RNA-seq on mESCs differentiated to embryoid body (4D Nucleome - Data Coordination...)

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