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A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design

Robin P Smith12, Samantha J Riesenfeld3, Alisha K Holloway3, Qiang Li126, Karl K Murphy12, Natalie M Feliciano12, Lorenzo Orecchia4, Nir Oksenberg12, Katherine S Pollard235* and Nadav Ahituv12*

Author Affiliations

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

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Genome Biology 2013, 14:R72  doi:10.1186/gb-2013-14-7-r72

Published: 18 July 2013

Additional files

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.

Format: XLSX Size: 14KB Download file

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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.

Format: XLSX Size: 21KB Download file

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