|
| Status |
Public on Jan 17, 2013 |
| Title |
Genome-wide quantitative enhancer activity maps identified by STARR-seq |
| Organisms |
Drosophila melanogaster; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Genomic enhancers are important regulators of gene expression, but their identification is a challenge and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, enabling screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type-specific enhancers across a broad continuum of strengths, linking differential gene expression to differences in enhancer activity and creating a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantitate enhancer activity in other eukaryotes, including human.
|
| |
|
| Overall design |
STARR-seq was performed in S2 and OSC cells with paired-end sequencing in two replicates and respective inputs. DHS-seq was done with single-end sequencing in two replicates for S2 and OSC cells. RNA-seq was performed with a strand-specific protocol using single-end sequencing in two replicates within S2 and OSC cells. STARR-seq was also performed in HeLa cells with single-end sequencing with a respective input.
|
| Web link |
http://starklab.org
|
| |
|
| Contributor(s) |
Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A |
| Citation(s) |
23328393, 25517091 |
| |
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
[email protected]
|
| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
|
| Department |
Global Computational Biology and Digital Sciences
|
| Street address |
Dr.-Boehringer-Gasse 5-11
|
| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
| |
|
| Platforms (3) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL11203 |
Illumina Genome Analyzer IIx (Drosophila melanogaster) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA175267 |
| SRA |
SRP015758 |
Less...
More...