 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 11, 2021 |
| Title |
4DNESB7XYI9V - sci-Hi-C on mESCs differentiated to embryoid body |
| Organism |
Mus musculus |
| Experiment type |
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.
|
| |
|
| Overall design |
lab: Christine Disteche, UW
award: 1U54DK107979-01
accession: 4DNESB7XYI9V
submitted_by: Giancarlo Bonora
dataset_label: sci-Hi-C on mESCs differentiated to embryoid body
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
experiment_type: sci-Hi-C
url: https://data.4dnucleome.org/experiment-sets/4DNESB7XYI9V/
number_of_experiments: 23
experiment: 4DNEXOA4DNR8; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXCDN76F9; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXJ33QCZU; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXLCFXRUP; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX1BY7H2C; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXU9FJ24U; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXTJOSWTW; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXMYV77X1; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXK2CP3J1; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXXNEYDTM; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXJNGKL32; replicate_number: Biorep 2, Techrep 1
experiment: 4DNEXJAHCEIN; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXLZWN9VH; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXV3C383J; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXB7EWKCM; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXTLVDZQP; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXEE1N4JI; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXPLD13JA; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXVG7LXZE; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXWHKWMSY; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXRMWXOKT; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXMN3ZJ4X; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXMNAHJPG; replicate_number: Biorep 2, Techrep 1
Series supplementary files:
***************
genome_assembly: GRCm38
description: A tarball containing processed sci-Hi-C data.
file name: 4DNFIZ8TEE2M.tar
file_format: tar
***************
file_type: readme
description: A text file describing the contents and processing steps for the sci-Hi-C processed data in 4DNFIZ8TEE2M.
file name: 4DNFI7QQWLOV.txt
file_format: txt
***************
file_type: directory tree
description: A text file with a directory tree for the sci-Hi-C processed data in 4DNFIZ8TEE2M.
file name: 4DNFICOPS6ER.txt
file_format: txt
|
| |
|
| Citation(s) |
34579774 |
|
Giancarlo Bonora et al. (2020) doi:10.1101/2020.11.20.390765
|
| |
| Submission date |
Oct 10, 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 (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (6)
|
| GSM5620573 |
4DNEXLCFXRUP (F123_d20), 4DNEXOA4DNR8 (TsixStop_d20), 4DNEXTJOSWTW (F121_d20) |
| GSM5620574 |
4DNEX1BY7H2C (F123_d7), 4DNEXCDN76F9 (TsixStop_d7), 4DNEXJ33QCZU (TsixStop_d0), 4DNEXMYV77X1 (F121_d7) |
| GSM5620575 |
4DNEXK2CP3J1 (F121_d0), 4DNEXU9FJ24U (F123_d0) |
| GSM5620576 |
4DNEXMN3ZJ4X (d0), 4DNEXRMWXOKT (d3), 4DNEXVG7LXZE (d11), 4DNEXWHKWMSY (d7) |
| GSM5620577 |
4DNEXEE1N4JI, 4DNEXMNAHJPG, 4DNEXJNGKL32, 4DNEXXNEYDTM, 4DNEXPLD13JA, 4DNEXTLVDZQP |
| GSM5620578 |
4DNEXB7EWKCM (TsixStop_d0), 4DNEXJAHCEIN (TsixStop_d11), 4DNEXLZWN9VH (TsixStop_d7), 4DNEXV3C383J (TsixStop_d3) |
|
| This SubSeries is part of SuperSeries: |
| GSE184554 |
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation |
|
| Relations |
| BioProject |
PRJNA770075 |
| SRA |
SRP340729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE185608_4DNFI7QQWLOV.txt.gz |
2.4 Kb |
(ftp)(http) |
TXT |
| GSE185608_4DNFICOPS6ER.txt.gz |
4.0 Kb |
(ftp)(http) |
TXT |
| GSE185608_4DNFIZ8TEE2M.tar.gz |
64.8 Mb |
(ftp)(http) |
TAR |
| GSE185608_RAW.tar |
20.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...