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| Status |
Public on Mar 15, 2013 |
| Title |
Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay |
| Organisms |
Escherichia coli; Homo sapiens |
| Experiment type |
Other
|
| Summary |
We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity.
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| Overall design |
Reporter mRNA-seq from HepG2 and K562 cells transfected with a ~55,000-plex MPRA plasmid pool containing 5,418 mutated human enhancer sequences, each linked to 10 distinct 10-nt tags. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers.
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| Contributor(s) |
Kheradpour P, Ernst J, Mikkelsen TS, Kellis M |
| Citation(s) |
23512712 |
| |
| Submission date |
Nov 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tarjei S Mikkelsen |
| Organization name |
Broad Institute
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
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| Samples (6)
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| Relations |
| SRA |
SRP009170 |
| BioProject |
PRJNA149003 |
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