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| Status |
Public on Dec 08, 2021 |
| Title |
Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue [Drosophila melanogaster] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
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| Summary |
Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.
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| Overall design |
We generated a population of Drosophila embryos in each of which reporter gene expression is driven by one genomically integrated reporter element from a pool of wild type enhancers or enhancers in which all binding sites for one or more selected TFs have been mutated. Each tested enhancer was tagged with several distinct 20-base degenerate sequence tags in the 3' UTR of the reporter gene. We dissociated embryonic cells and FACS-sorted informative populations, and reporter gene molecules were counted by a Unique Molecular Identifier (UMI) amplification strategy. We detected RNA and DNA levels by high-throughput sequencing of tagged reporter gene amplicons and normalized gene expression (RNA UMI counts) by dividing by DNA UMI counts to generate a measure of enhancer activity.
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| Contributor(s) |
Waters CT, Gisselbrecht SS, Sytnikova YA, Cafarelli TM, Hill DE, Bulyk ML |
| Citation(s) |
34930411 |
| |
| Submission date |
May 05, 2020 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Stephen Gisselbrecht |
| E-mail(s) |
steveg@alum.mit.edu
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| Phone |
857-540-2853
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| Organization name |
Brigham and Women's Hospital
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| Department |
Division of Genetics, Department of Medicine
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| Lab |
Martha L. Bulyk
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| Street address |
77 Avenue Louis Pasteur, Rm 468
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (18)
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| This SubSeries is part of SuperSeries: |
| GSE149908 |
Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue |
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| Relations |
| BioProject |
PRJNA630468 |
| SRA |
SRP260103 |
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