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Series GSE184554 Query DataSets for GSE184554
Status Public on Sep 24, 2021
Title Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary 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. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.

### Competing Interest Statement

The authors have declared no competing interest.

### This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series
 
Citation(s) 34579774
Submission date Sep 21, 2021
Last update date Oct 22, 2021
Contact name 4DN DCIC
E-mail(s) support@4dnucleome.org
Organization name 4D Nucleome - Data Coordination and Integration Center
Street address 10 Shattuck St
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (25)
GSM5593361 sci-ATAC-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXUTXVJNS
GSM5593362 sci-ATAC-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXOSQFCTM
GSM5593363 sci-ATAC-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXXXQ7SNN
This SuperSeries is composed of the following SubSeries:
GSE184600 4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body
GSE184602 4DNESCX7WHJ1 - sci-RNA-seq on mESCs differentiated to embryoid body
GSE185608 4DNESB7XYI9V - sci-Hi-C on mESCs differentiated to embryoid body
Relations
BioProject PRJNA765363

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE184554_RAW.tar 20.0 Kb (http)(custom) TAR (of TXT)
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