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Documentation: Allen Mouse Brain Atlas

Document	Description
In Situ Hybridization	Processes and procedures used to perform ISH
Informatics Data Processing	Design and implementation of the Informatics Data Pipeline (IDP)
Reference Atlas, Version 1 (2008)	Overview of the sagittal and coronal Allen Reference Atlases
Reference Atlas, Version 2 (2011)	Overview of the sagittal and coronal Allen Reference Atlases
Mouse CCF, Reference Atlas, Version 3 (2015)	Overview of the design and implementation of the Allen Mouse Common Coordinate Framework
Fine Structure Annotation	Explanation of the informatics methods used to create the fine structure annotations
Acknowledgement of Collaborators	Recognition of collaborators and others who provided assistance

Supplemental Data: Allen Mouse Brain Atlas

Document	Description
ISH Platform Controls	Quality control standards for high-throughput RNA in situ hybridization data generation
Cross Platform Validation	Methods for validating the data
AGEA User Guide	Overview of the Anatomic Gene Expression Atlas (AGEA)
Sleep Study	PDF Article of the Sleep Study Results
Mouse Strains Study	Mouse Strains Study
FSA Reports	Compilations of neuroanatomic and gene expression characteristics for key brain regions or nuclei
Somatosensory Annotation	Technical white paper detailing the methods used to manually annotate the expression patterns of genes in the mouse somatosensory cortex
Comparison of the Top 1000 Genes	The 1000 most requested genes were analyzed as a validation of the ISH data
Comparison of the Top 1000 Genes (Oct 2010)	An updated list of the 1000 most requested genes that were analyzed as a validation of the ISH data