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| Status |
Public on Sep 04, 2012 |
| Title |
Robust 4C-seq data analysis to screen for regulatory DNA interactions |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Regulatory DNA elements can control expression of distant genes via physical interactions. Here, we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using Chromosome Conformation Capture combined with high-throughput sequencing (4C-seq) data. Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.
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| Overall design |
A high resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline was applied to several viewpoints in four genomic loci (the well-characterized alpha-globin and beta-globin loci, and the novel Oct4 and Satb1 loci), allowing robust detection of physical interactions between regulatory DNA elements.
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| Contributor(s) |
Landan G, van de Werken H |
| Citation(s) |
22961246 |
| |
| Submission date |
Aug 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gilad Landan |
| E-mail(s) |
gilad.landan@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
234 Herzl Street
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA174285 |
| SRA |
SRP015352 |
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