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| Status |
Public on Sep 24, 2021 |
| Title |
4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| 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.
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| Overall design |
lab: Christine Disteche, UW
award: 1U54DK107979-01
accession: 4DNESOUYRIO9
submitted_by: Giancarlo Bonora
dataset_label: sci-ATAC-seq on mESCs differentiated to embryoid body
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
experiment_type: sci-ATAC-seq
url: https://data.4dnucleome.org/experiment-sets/4DNESOUYRIO9/
number_of_experiments: 9
experiment: 4DNEXUTXVJNS; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXOSQFCTM; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXXXQ7SNN; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXMJVA3ZW; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXP788IVD; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXOLF62PK; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXOKNIX5B; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXX4XDGPO; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX55NM5L3; replicate_number: Biorep 1, Techrep 1
Series supplementary files:
***************
genome_assembly: GRCm38
description: A tarball containing processed sci-ATAC-seq data.
file name: 4DNFI3GQKK43.tar
file_format: tar
***************
file_type: readme
description: A text file describing the contents and processing steps for the sci-ATAC-seq processed data in 4DNFI3GQKK43.
file name: 4DNFIEIH3BBX.txt
file_format: txt
***************
file_type: directory tree
description: A text file with a directory tree for the sci-ATAC-seq processed data in 4DNFI3GQKK43.
file name: 4DNFIB8E2QM9.txt
file_format: txt
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| Citation(s) |
34579774 |
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Giancarlo Bonora et al. (2020) doi:10.1101/2020.11.20.390765
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| Submission date |
Sep 22, 2021 |
| Last update date |
Sep 29, 2021 |
| Contact name |
4DN DCIC |
| E-mail(s) |
support@4dnucleome.org
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| Organization name |
4D Nucleome - Data Coordination and Integration Center
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| Street address |
10 Shattuck St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (9)
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| 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 |
| GSM5593364 |
sci-ATAC-seq on F123-CASTx129 - 4DNEXMJVA3ZW |
| GSM5593365 |
sci-ATAC-seq on F121-6-CASTx129 differentiated to neuronal stem cell - 4DNEXP788IVD |
| GSM5593366 |
sci-ATAC-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXOLF62PK |
| GSM5593367 |
sci-ATAC-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXOKNIX5B |
| GSM5593368 |
sci-ATAC-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXX4XDGPO |
| GSM5593369 |
sci-ATAC-seq on F121-6-CASTx129 - 4DNEX55NM5L3 |
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| This SubSeries is part of SuperSeries: |
| GSE184554 |
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation |
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| Relations |
| BioProject |
PRJNA765361 |
| SRA |
SRP338255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE184600_4DNFI3GQKK43.tar.gz |
344.7 Mb |
(ftp)(http) |
TAR |
| GSE184600_4DNFIB8E2QM9.txt.gz |
382 b |
(ftp)(http) |
TXT |
| GSE184600_4DNFIEIH3BBX.txt.gz |
1.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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