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| Status |
Public on Mar 01, 2023 |
| Title |
Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture, ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.
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| Overall design |
ChIP-seq, 4C-seq and RNA-seq experiments were performed on both wildtype and DNA-fragment editting cell lines (mE1 insertion, mE2 insertion and ac1 repeat). For ChIP-seq experiments, Binding patterns of CTCF and Cohesin complex(showed by Rad21) as well as histone modification marker H3K27ac were examined. For 4C-seq experiments, the 3D chromatin conformations of several viewpoints were captured by 4C (Circular Chromatin Conformation Capture) method, in duplicate. For RNA-seq experiments, the mRNA profiles of these cell lines were generated by deep sequencing, in duplicate.
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| Contributor(s) |
Wu Y, Jia Z, Ge X |
| Citation(s) |
32249388 |
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| Submission date |
Mar 20, 2020 |
| Last update date |
Jun 02, 2023 |
| Contact name |
yonghu wu |
| E-mail(s) |
yonghuwu88@gmail.com
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| Phone |
+8615921739862
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| Organization name |
Shanghai JiaoTong University
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| Street address |
800# Dongchuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platforms (1) |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE147286 |
Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus |
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| Relations |
| BioProject |
PRJNA613659 |
| SRA |
SRP253476 |
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