Supplementary information
From the following article:
Genome-wide atlas of gene expression in the adult mouse brain
Ed S. Lein, Michael J. Hawrylycz, Nancy Ao, Mikael Ayres, Amy Bensinger, Amy Bernard, Andrew F. Boe, Mark S. Boguski, Kevin S. Brockway, Emi J. Byrnes, Lin Chen, Li Chen, Tsuey-Ming Chen, Mei Chi Chin, Jimmy Chong, Brian E. Crook, Aneta Czaplinska, Chinh N. Dang, Suvro Datta, Nick R. Dee, Aimee L. Desaki, Tsega Desta, Ellen Diep, Tim A. Dolbeare, Matthew J. Donelan, Hong-Wei Dong, Jennifer G. Dougherty, Ben J. Duncan, Amanda J. Ebbert, Gregor Eichele, Lili K. Estin, Casey Faber, Benjamin A. Facer, Rick Fields, Shanna R. Fischer, Tim P. Fliss, Cliff Frensley, Sabrina N. Gates, Katie J. Glattfelder, Kevin R. Halverson, Matthew R. Hart, John G. Hohmann, Maureen P. Howell, Darren P. Jeung, Rebecca A. Johnson, Patrick T. Karr, Reena Kawal, Jolene M. Kidney, Rachel H. Knapik, Chihchau L. Kuan, James H. Lake, Annabel R. Laramee, Kirk D. Larsen, Christopher Lau, Tracy A. Lemon, Agnes J. Liang, Ying Liu, Lon T. Luong, Jesse Michaels, Judith J. Morgan, Rebecca J. Morgan, Marty T. Mortrud, Nerick F. Mosqueda, Lydia L. Ng, Randy Ng, Geralyn J. Orta, Caroline C. Overly, Tu H. Pak, Sheana E. Parry, Sayan D. Pathak, Owen C. Pearson, Ralph B. Puchalski, Zackery L. Riley, Hannah R. Rockett, Stephen A. Rowland, Joshua J. Royall, Marcos J. Ruiz, Nadia R. Sarno, Katherine Schaffnit, Nadiya V. Shapovalova, Taz Sivisay, Clifford R. Slaughterbeck, Simon C. Smith, Kimberly A. Smith, Bryan I. Smith, Andy J. Sodt, Nick N. Stewart, Kenda-Ruth Stumpf, Susan M. Sunkin, Madhavi Sutram, Angelene Tam, Carey D. Teemer, Christina Thaller, Carol L. Thompson, Lee R. Varnam, Axel Visel, Ray M. Whitlock, Paul E. Wohnoutka, Crissa K. Wolkey, Victoria Y. Wong, Matthew Wood, Murat B. Yaylaoglu, Rob C. Young, Brian L. Youngstrom, Xu Feng Yuan, Bin Zhang, Theresa A. Zwingman & Allan R. Jones
Nature 445, 168-176(11 January 2007)
doi:10.1038/nature05453
Supplemental Methods 1
Detailed methodologies for tissue processing, probe design and generation, data generation, and image acquisition used for the Allen Brain Atlas project
Supplemental Methods 2
Detailed methodologies for informatics-based image quantification and mapping of ISH data to a common 3D coordinate system for genome-wide analysis
Supplemental Methods 3
Detailed methodologies used to generate the Allen Reference Atlas
Supplemental Methods 4
Description of methods used for voxel-based correlation analysis
Supplemental Data 1
Comparison of non-isotopic in situ hybridization (ISH) data generated for the Allen Brain Atlas project to comparable radioactive ISH data from other sources
Supplemental Data 2
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
Supplemental Data 3
Control data demonstrating the reproducibility of the ABA ISH platform across conditions and across the duration of the ABA project
Supplemental Data 4
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
Supplemental Data 5
Detailed expert annotation of the complete ligand-gated ion channel family in layers of the neocortex. Accompanies Supplemental Data 4
Supplemental Figure 1
Genome-wide analysis of expression level vs. percentage of expressing cells in 12 major brain regions
Supplementary Table 1
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
Supplemental Table 2
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
Supplemental Table 3
Genes identified as the most specific for each of 12 different major brain regions
Supplemental Table 4
Genes displaying mRNA targeting to dendrites (neurons) or processes (non-neuronal cells)
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