A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
- Equal contributors
1 Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
2 Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
3 Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA
4 Division of Biostatistics, University of California San Francisco, 1650 Owens St, CA 94158, USA
5 Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
6 Current address: Institute for Pediatrics, Translational Research Center for Development and Disease, Children's Hospital of Fudan University, Shanghai, 201102, China
Genome Biology 2013, 14:R72 doi:10.1186/gb-2013-14-7-r72Published: 18 July 2013
Additional file 1:
Supplemental note. Two results that justify and give a mathematical proof of correctness of our formal algorithm (in box), which we used to construct the oligomer library.
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Additional file 2:
Supplemental figures. Seven supplemental figures and legends.
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Additional file 3:
Supplemental Table 1. Multiplexed sequence screen data for 184 constructs tested using zebrafish transgenic assays.
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Additional file 4:
Supplemental Table 2. Embryo counts from the functional dissection experiments.
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Additional file 5:
Supplemental Table 3. Enriched gene ontology terms for 15-bp alignments of the four tissue-specific multiplexed oligomers.
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Additional file 6:
Supplemental Table 4. Enriched gene ontology terms for 9-bp (+2 flanking bp) alignments of the three tissue-specific multiplexed oligomers.
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Additional file 7:
Supplemental Table 5. Genomic position and embryo counts for the thirty approximately 1,000-bp regions tested for enhancer activity.
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