Supplementary Materials

for Lein, E.S., Hawrylycz, M.J. et. al. (2007) Genome-wide atlas of gene expression in the adult mouse brain.  Nature 445:168-176, doi:10.1038/nature05453

1. Detailed methodologies for tissue processing, probe design and generation, data generation, and image acquisition used for the Allen Brain Atlas project
2. Detailed methodologies for informatics-based image quantification and mapping of ISH data to a common 3D coordinate system for genome-wide analysis
3. Detailed methodologies used to generate the Allen Reference Atlas
4. Description of methods used for voxel-based correlation analysis
5. Comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data from other sources
6. Side-by-side image comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data. Accompanies Supplemental Data 1
7. Control data demonstrating the reproducibility of the ABA ISH platform across conditions and across the duration of the ABA project
8. Comparison of expression patterns of the ligand-gated ion channel family to available literature and other data sources, as well as methodology for fine-detailed expert annotation of the ligand-gated ion channel family in the neocortex
9. Detailed expert annotation of the complete ligand-gated ion channel family in layers of the neocortex. Accompanies Supplemental Data 4
10. Genome-wide analysis of expression level vs. percentage of expressing cells in 12 major brain regions
11. Genes enriched in major cell populations in the brain (neurons, oligodendrocytes, astrocytes, and choroid plexus cells) identified through correlation-based searches seeded with cell-type specific gene expression patterns. Also included are genes with apparent ubiquity as well as genes that do not have detectable expression in the brain
12. Gene Ontology (GO) categories over-represented in genes enriched in major neural cell types and in genes that are either apparently ubiquitous or not expressed. Accompanies Supplemental Table 1
13. Genes identified as the most specific for each of 12 different major brain regions
14. Genes displaying mRNA targeting to dendrites (neurons) or processes (non-neuronal cells)