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| Status |
Public on Mar 05, 2023 |
| Title |
Transcription factor interactions explain the context-dependent activity of CRX binding sites |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Other
|
| Summary |
We assessed how the effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory sequence (CRS) depend on the local sequence context. We constructed a library of synthetic CRSs composed of TFBSs enriched in mouse photoreceptors and assayed them by massively parallel reporter assay in live mouse retina. We used the resulting data to train neural network-based models that predict CRS activity from sequence.
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| Overall design |
A library of 6600 barcoded reporter gene plasmids were transfected into mouse retinas. Three replicates were performed. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.
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| Contributor(s) |
White MA, Loell KJ, Friedman RZ |
| Citation(s) |
38227575 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM121755 |
DISCOVERY OF DNA DETERMINANTS OF TRANSCRIPTION FACTOR BINDING AND FUNCTION IN PHO |
WASHINGTON UNIVERSITY |
Michael Aaron White |
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| |
| Submission date |
Feb 22, 2023 |
| Last update date |
Feb 06, 2024 |
| Contact name |
Michael Aaron White |
| E-mail(s) |
mawhite@wustl.edu
|
| Organization name |
Washington University in St. Louis School of Medicine
|
| Department |
Genetics
|
| Street address |
660 South Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63144 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA937735 |
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