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Status |
Public on May 01, 2024 |
Title |
Single-cell RNA-seq analysis of mouse embryonic stem cells before and after Cohesin depletion |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
The contrast between the disruption of genome topology upon cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic co-expression tendency of cis-linked genes in single cells. Notably, through single-cell RNA-seq profiling of genes in mouse embryonic stem cells, we found that cohesin loss induces widespread gene co-activation in cis. Our results support that cohesin arranges nuclear topology to control gene co-expression in single cells.
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Overall design |
JM8.N4 mouse embryonic stem cells (mESCs) from the C57BL/6N strain were edited by using CRISPR/Cas9 to fuse cohesin subunit RAD21 to the auxin-induced degron (AID) system. The derived cells were used in Smart-SCRB (Smart-Single Cell RNA Barcoding, a highly sensitive single-cell transcriptome assay) analysis and single-cell ATAC-seq analysis under control and acute cohesin loss (6hrs after the auxin treatment) conditions.
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Contributor(s) |
Dong P, Liu ZJ |
Citation missing |
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Submission date |
Apr 23, 2024 |
Last update date |
May 01, 2024 |
Contact name |
PENG DONG |
E-mail(s) |
p.dong@siat.ac.cn
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Organization name |
Shenzhen Institute of Advanced Technology
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Street address |
1068 Xueyuan Avenue, Shenzhen University Town
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City |
Shenzhen |
State/province |
Guangdong |
ZIP/Postal code |
518055 |
Country |
China |
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Platforms (1) |
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Samples (3) |
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Relations |
BioProject |
PRJNA1103738 |