A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

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The Cre/lox system is widely used in mice to achieve cell-type-specific gene expression. However, a strong and universally responding system to express genes under Cre control is still lacking. We have generated a set of Cre reporter mice with strong, ubiquitous expression of fluorescent proteins of different spectra. The robust native fluorescence of these reporters enables direct visualization of fine dendritic structures and axonal projections of the labeled neurons, which is useful in mapping neuronal circuitry, imaging and tracking specific cell populations in vivo. Using these reporters and a high-throughput in situ hybridization platform, we are systematically profiling Cre-directed gene expression throughout the mouse brain in several Cre-driver lines, including new Cre lines targeting different cell types in the cortex. Our expression data are displayed in a public online database to help researchers assess the utility of various Cre-driver lines for cell-type-specific genetic manipulation.

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Figure 1: Generation of the Cre-reporter lines.
Figure 2: Significantly enhanced fluorescent labeling in the new reporter lines.
Figure 3: Informatics processing of the ISH characterization data.
Figure 4: New Cre lines and their differential recombination patterns in different cortical cell types.
Figure 5: Comparison of recombination patterns in two closely related knock-in Cre lines, Pvalb-IRES-Cre and Pvalb-2A-Cre.


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We are grateful for the professional support of the entire Atlas production team, led by P. Wohnoutka, and the Information Technology team, led by C. Dang, at the Allen Institute, without which the work would have not been possible to accomplish. We are thankful to A. Bernard for her contribution in establishing the DFISH process, L. Kuan for ISH data quantification and R. Hunter for coordinating transgenic mice production. We also gratefully acknowledge the following researchers for providing various research materials: R. Tsien (University of California at San Diego) for the tdTomato DNA construct, L. Luo (Stanford University) for the Rosa-CAG targeting construct, K. Deisseroth (Stanford University) for the WPRE-containing DNA construct, B. Sauer (National Institute of Diabetes and Digestive and Kidney Diseases) via Addgene for the Cre and EGFP-Cre DNA constructs, P. Chambon (Institut de Génétique et de Biologie Moléculaire et Cellulaire) for the CreERT2 DNA construct, P. Soriano (Fred Hutchinson Cancer Research Center) via Addgene for the PhiC31o, FLPo and pPGKneotpAlox2 DNA constructs, A. Nagy (Mount Sinai Hospital in Toronto) for the G4 ES cell line, G. Oliver (St. Jude's Children's Research Hospital) for the Six3-Cre mice, N. Heintz (Rockefeller University) via Mutant Mouse Regional Resource Centers (MMRRC) for the Ntsr1-Cre mice and X. Zhuang (University of Chicago) for the Slc6a3-Cre mice. The authors thank the Allen Institute founders, P.G. Allen and J. Patton, for their vision, encouragement and support. This work was funded by the Allen Institute for Brain Science and a US National Institutes of Health grant (MH085500) to H.Z.

Author information

H.Z. designed the study, analyzed data and wrote the paper. L.M. generated the Cre reporter lines and the knock-in Cre driver lines. T.A.Z. and E.S.L. designed and generated the BAC transgenic Cre driver lines. H.Z., S.M.S. and T.A.Z. set up the characterization pipeline and database. S.W.O. produced and performed experiments with rAAVs. H.A.Z. performed in vivo two-photon imaging experiments. M.J.H. and L.L.N. conducted informatics analysis. H.G. assisted with transgenic mice production and characterization. R.D.P. provided lab resources and scientific advice. A.R.J. provided institutional support.

Correspondence to Hongkui Zeng.

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