1. Copyright OpenHelix. No use or reproduction without express written consent1

2. The Allen Mouse Brain Atlas From the Allen Institute for Brain Science Materials prepared by: Cynthia Perreault-Micale, Ph.D. Dorothy S. Reilly, Ph.D. www.openhelix.com Updated: Q3 2011 Version 2

3. Copyright OpenHelix. No use or reproduction without express written consent3 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

4. Copyright OpenHelix. No use or reproduction without express written consent4 Many Allen Brain Atlas Resources The Allen Brain Atlas portal: http://www.brain-map.org Mouse Spinal Cord Developing Mouse Brain

5. Copyright OpenHelix. No use or reproduction without express written consent5 The Allen Institute for Brain Science, cont. Allen Human Brain Atlas Transgenic Mouse Sleep The Allen Brain Atlas portal: http://www.brain-map.org

6. Copyright OpenHelix. No use or reproduction without express written consent6 Mouse Brain Atlas The Allen Mouse Brain Atlas: http://mouse.brain-map.org/welcome.do Navigation Menus Menu Instructions Browse by Structure or Gene Symbol Search Options

7. Copyright OpenHelix. No use or reproduction without express written consent7 Allen Mouse Brain Atlas Content & Organization 8-week old C57Bl/6J male mouse brain(s) Allen Reference Atlas: anatomical reference gene expression data: non-isotopic in situ hybridization coronal: divides anterior & posterior sagittal: divides left & right sides horizontal or transverse Key for images:

8. Copyright OpenHelix. No use or reproduction without express written consent8 Allen Mouse Brain Atlas Publications Genome Biology 9:R23, 2008 BMC Bioinformatics 9:153, 2008 Biol.Cell 99:403, 2007

9. Copyright OpenHelix. No use or reproduction without express written consent9 Allen Mouse Brain Atlas Documentation & Help The Allen Mouse Brain Atlas: http://mouse.brain-map.org/welcome.do

10. Copyright OpenHelix. No use or reproduction without express written consent10 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

11. Copyright OpenHelix. No use or reproduction without express written consent11 Accessing The Allen Reference Atlas The Allen Mouse Brain Atlas: http://mouse.brain-map.org/welcome.do

12. Copyright OpenHelix. No use or reproduction without express written consent12 Allen Reference Atlas Click to enlarge

13. Copyright OpenHelix. No use or reproduction without express written consent13 Allen Reference Atlas: Structure Browser dentate gyrus Browse by structure Search by structure Toggle between Sagittal & Coronal, click ? for help

14. Copyright OpenHelix. No use or reproduction without express written consent14 Allen Reference Atlas: Structure Search Results Zoomed Atlas

15. Copyright OpenHelix. No use or reproduction without express written consent15 Allen Reference Atlas: Atlas Locations Click here

16. Copyright OpenHelix. No use or reproduction without express written consent16 ARA Structures: Dentate gyrus

17. Copyright OpenHelix. No use or reproduction without express written consent17 Legend & Structural Relationships Colors match atlas images & also indicate structurally related regions

18. Copyright OpenHelix. No use or reproduction without express written consent18 ARA Structures: Show Nissl Entire field will be changed to Nissl stained image

19. Copyright OpenHelix. No use or reproduction without express written consent19 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

20. Copyright OpenHelix. No use or reproduction without express written consent20 Allen Mouse Brain Atlas Search Options Search Options Detailed search instructions The Allen Mouse Brain Atlas: http://mouse.brain-map.org/welcome.do http://genome.ucsc.edu/cgi-bin/hgVisiGene

21. Copyright OpenHelix. No use or reproduction without express written consent21 Allen Mouse Brain Atlas Gene Search myelin Mag, Mal, Mbp, Stard8 The Allen Mouse Brain Atlas: http://mouse.brain-map.org/welcome.do

22. Copyright OpenHelix. No use or reproduction without express written consent22 Allen Mouse Brain Atlas Anatomic Search Our example - Olfactory bulb, high expression, high density, clustered pattern Definition: “Expression density is the ratio of the number of labeled cells to the total number of cells in a structure...” Find calculation descriptions here on Allen Mouse Brain Atlas homepage

23. Copyright OpenHelix. No use or reproduction without express written consent23 Anatomic Search Additional Specifications Olfactory bulb, high expression, high density, clustered pattern Boolean operator “AND” Cerebral cortex, low/medium expression, low/medium density, any pattern Click results

24. Copyright OpenHelix. No use or reproduction without express written consent24 Fine Structure Annotation Search Definition: “Fine structure annotation lists are genes that have high specificity expression in particular regions or nuclei” Example - high expression specific to Cerebral cortex, layers 2-3 Link here from Allen Mouse Brain Atlas homepage Click results

25. Copyright OpenHelix. No use or reproduction without express written consent25 Allen Mouse Brain Boolean Syntax Query Our example - gene name includes “peptidase” AND cerebellum, high expression genename~*peptidase* AND structac=CB[xlevel=2] High expression = 2, low/medium expression = 1 results

26. Copyright OpenHelix. No use or reproduction without express written consent26 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

27. Copyright OpenHelix. No use or reproduction without express written consent27 Allen Mouse Brain Atlas Anatomic Search Results Three types of info from Gene Info link - 1. Gene name, symbol, synonym & species 2. External resources - database links 3. Image series & expression info (next slide) 1 2

28. Copyright OpenHelix. No use or reproduction without express written consent28 Search Results: Gene Expression & Image Summary Gene Info: Links to Ppfibp1 (liprin beta 1) Images Expression summary: click to display image for specific structure Experimental Details Options to mouse over summary bars to see image in window Change view from top right menu bar 3 Change view

29. Copyright OpenHelix. No use or reproduction without express written consent29 Anatomic Search Results, Available Images Click to see images available

30. Copyright OpenHelix. No use or reproduction without express written consent30 Anatomic Search Results, More Details 3D image files viewed with Brain Explorer application Links to summary of expression levels Use “Add” to select images to examine further

31. Copyright OpenHelix. No use or reproduction without express written consent31 List View: Select Images Your selections are added here

32. Copyright OpenHelix. No use or reproduction without express written consent32 List View: Add Genes

33. Copyright OpenHelix. No use or reproduction without express written consent33 Select Thumbnail View Pcdh21 - protocadherin 21 Nab1 - Ngfi-A binding protein 1 Ppfibp1 - PTPRF interacting protein, binding protein 1 (liprin beta 1) A quick overview of these images

34. Copyright OpenHelix. No use or reproduction without express written consent34 Thumbnail View: ISH Click

35. Copyright OpenHelix. No use or reproduction without express written consent35 Thumbnail View: Single Image Viewer Click to open in Single Image Viewer Key

36. Copyright OpenHelix. No use or reproduction without express written consent36 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

37. Copyright OpenHelix. No use or reproduction without express written consent37 Search Results: View Detailed Images Click to open the Multiple Image Viewer

38. Copyright OpenHelix. No use or reproduction without express written consent38 Multiple Image Viewer Ppfibp1 image set Cdh21 image set Nab1 image set

39. Copyright OpenHelix. No use or reproduction without express written consent39 Multiple Image Viewer, with Coronal Atlas Drag and drop panels to optimize layout of display Coronal Atlas click & drag panels

40. Copyright OpenHelix. No use or reproduction without express written consent40 Multiple Image Viewer: Additional Display Options additional display options click scroll

41. Copyright OpenHelix. No use or reproduction without express written consent41 Multiple Image Viewer: Image Controls Single high resolution Synchronize views Image summary Close panel Image altered contrast

42. Copyright OpenHelix. No use or reproduction without express written consent42 Multiple Image Viewer: Compare Gene Expression Single high resolution Synchronize views Image summary Close panel Synchronized sections in all four datasets click

43. Copyright OpenHelix. No use or reproduction without express written consent43 Multiple Image Viewer: Compare Gene Expression Single high resolution Synchronize views Image summary Close panel Drag to overlay panels - compare Gene to Atlas Overlay of both images drag

44. Copyright OpenHelix. No use or reproduction without express written consent44 Multiple Image Viewer: Compare Gene Expression Single high resolution Synchronize views Image summary Close panel Drag to overlay panels - compare Gene to Atlas High resolution view Image summary

45. Copyright OpenHelix. No use or reproduction without express written consent45 Multiple Image Viewer: Compare Gene Expression Single high resolution Synchronize views Image summary Close panel Allen Brain Atlas Legend Atlas Legend Change views

46. Copyright OpenHelix. No use or reproduction without express written consent46 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

47. Advanced Features: Download Brain Explorer App After installation the Allen Mouse Brain Atlas Brain Explorer application & tutorial both open The Allen Mouse Brain Atlas: http://mouse.brain-map.org 3D file coronal plane Pcdh21 protocadherin 21 Copyright OpenHelix. No use or reproduction without express written consent47

48. Copyright OpenHelix. No use or reproduction without express written consent48 Advanced Features: Brain Explorer Viewing Options 3D file coronal plane Pcdh21 protocadherin 21 View 3D image Rotate image Click on anatomical region Add reference image

49. Copyright OpenHelix. No use or reproduction without express written consent49 Advanced Features: More Brain Explorer Options 3D file coronal plane Pcdh21 protocadherin 21 http://bit.ly/aba_explorer

50. Copyright OpenHelix. No use or reproduction without express written consent50 Advanced Features: AGEA From AGEA Tutorial

51. Copyright OpenHelix. No use or reproduction without express written consent51 AGEA: Anatomic Gene Expression Atlas

52. Copyright OpenHelix. No use or reproduction without express written consent52 Advanced Features: API Allen Mouse Brain Atlas Application Programming Interface (API)

53. Copyright OpenHelix. No use or reproduction without express written consent53 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

54. Copyright OpenHelix. No use or reproduction without express written consent54 Summary Neuroanatomy ontology The Allen Brain Atlas: http://www.brain-map.org Detailed annotation of anatomic structures

55. Copyright OpenHelix. No use or reproduction without express written consent55 Many Searching & Viewing Options Searches Multiple image viewer Anatomic Gene Expression Atlas (AGEA) Brain Explorer application

56. Copyright OpenHelix. No use or reproduction without express written consent56 The Allen Mouse Brain Atlas Agenda Introduction and Credits Allen Reference Atlas Search Options Understanding Results Image Viewer Advanced Features Summary Exercises The Allen Brain Atlas portal: http://www.brain-map.org

57. Copyright OpenHelix. No use or reproduction without express written consent57