1. Supported by the NSF Plant Genome Research and REU Programs *Supported by the NSF Plant Genome Research and REU Programs A tutorial on the Cell Wall Genomics website Bryan Penning

2. Supported by the NSF Plant Genome Research and REU Programs Overview We will give a guided tutorial of the site and how to access its information –Guided tutorial – basic features of our site –Guided tutorial – Fourier Transform Infrared (FTIR) data –Guided tutorial – using the gene family trees at our site After this tutorial –You will have an understanding of why this was undertaken –You will be able to use the information available on our site

3. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: Main Page Between the blue bars are descriptions and links to three cell wall sites. Top: Oligogo at U. Wisconsin for tested primers to the SALK lines. Middle: CWG at Purdue for FTIR data, this site. Bottom: UniformMu at U. Florida for information on maize mutator mutants in a W22 background The main page provides links to tutorials The main parts of our site can be accessed using the links in the upper left hand corner of our site A drop-down menu with links to our group is located at the bottom of the website

4. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: Introduction and Cell Wall The introduction page gives background information on cell walls and highlights some methods used to study them The cell wall page gives a brief overview of plant cell walls and their architecture including the major differences between Type I cell walls found in Arabidopsis thaliana and Type II cell walls found in maize and rice

5. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG mutants The Literature page lists known mutants classified into one of six classes (Class 1 shown) Clicking on 1.1 opens a page of all known mutants for Class 1.1 (MUR1 is shown) Each mutant has photos and hypertext links to papers relevant to the mutant where available

6. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families The largest concentration of information at our site is contained in the CWG families section Genes are classified into six families plus an unknowns section Clickable links open a page showing all of the known genes for that family in table and dendrogram (tree) form Clicking on 1.1 takes you to the next page…

7. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Family 1.1 opens a new page with tree diagrams for Arabidopsis, rice, maize, and a combined dendrogram (direct links to their spot on the page are at the top) Each tree image can be clicked to open a FLASH page Below each image is a link to open the protein sequences of the family members (You can right click and choose “save as” to download the sequence information)

8. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Below the Arabidopsis tree is a brief family description and a table The table lists each gene member and if available: common name, SALK lines, and a number of columns to describe the FTIR spectra type (information on FTIR data can be found later in the tutorial) The gene names are a hypertext link leading to Oligogo (see next page)

9. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on a gene name in the table takes you to an outside link - the Wisconsin T-DNA project (Oligogo) by O’Malley and Patterson Gene At3g62830 is shown above where primers for SALK insertions of that gene are listed and can be ordered

10. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: FTIR Data On the families table are links to excel files of wild type and mutant spectral data (see our FTIR tutorial for more information http://cellwall.genomics.purdue.edu/) http://cellwall.genomics.purdue.edu/ Listed are the number of principal components that give greatest separation and the % of individuals correctly classified A yes/no/maybe spectrotype (yes >80%, 80% ≤ maybe ≥ 70%, no < 70%) is given with a link to interpreted data if there is a mutant spectrotype

11. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: FTIR Data Page Information contained in the PDF Files for FTIR (likely spectrotype) –Name and our data interpretation –Top left: Avg. spectra of mutant and Wt (Col) –Top right: Digital subtraction of mutant from Wt –Bottom left: PCA cluster plot showing separation –Bottom Right: PC Loading(s) contributing most to separation –See FTIR tutorial for more information http://cellwall.genomics.pur due.edu/ http://cellwall.genomics.pur due.edu/

12. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: NIR Data Maize mutants showing a NIR mutant phenotype –You can download the wildtype spectra from the W22 Spectra column –You can download the mutant spectra from the Mutant Spectra column –You can see our annotation in the Spectrotype column (next slide) –See Techniques VIII for details on NIR: http://cellwall.genomi cs.purdue.edu/techni ques/8.html http://cellwall.genomi cs.purdue.edu/techni ques/8.html

13. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: NIR Data Page Information contained in the PDF Files for FTIR –Family: Name as listed in the Maize family data table –Interpretation: Our evaluation of the data for important peaks –PLS loading: Differences in spectral values between mutant and wildtype –PLS score plot: shows separation of particular reads for mutant and wildtype

14. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking the Arabidopsis tree opens a FLASH file family tree as a radial dendrogram with colored ovals denoting tree clades of similar sequence (1.1 shown) See how these trees are made with our Tree Tutorial: http://cellwall.genomics.purdue. edu/ http://cellwall.genomics.purdue. edu/ Each oval can be clicked to open a close up view of the individual clade, such as AUD/SUD (next page)…

15. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families In this view the AUD/SUD clade of 1.1 is shown as a radial dendrogram Clicking any gene name will bring up a drop down menu with links to information outside of our site For Arabidopsis, we link to TIGR, MIPs, TAIR, and SALK Clicking on any of these links will open a gene information page in a new window from that source

16. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on the TIGR button opens a gene information page from The Institute for Genomic Research From this page you can download the Genomic, cDNA, or protein sequence for this gene and find out some basic information as to its classification and attributes

17. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on the MIPs button opens a page from the Munich Information Center for Protein sequences This site will give you any known information about the protein

18. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on the TAIR button opens a page from The Arabidopsis Information Resource TAIR includes a host of links and useful information on a number of topics such as annotations, bibliographies, map positions, gene model information, gene ontogeny, and general information

19. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on the SALK button opens a page from SIGnAL (the SALK Institute Genomic Analysis Laboratory) This page shows all of the SALK T-DNA insertions and their location in the gene (a vertical line runs down the center of the gene and through the SALK boxes)

20. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families As with the Arabidopsis tree, you can click on the Rice tree to bring up an interactive FLASH file of a radial dendrogram family tree (1.1 shown) Clicking on the individual clades of the radial dendrogram brings up a closer view such as AUD- SUD-like…

21. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on the AUD-SUD clade brings up a close-up view of that part of the tree as a radial dendrogram There are clickable links for each gene member The links for TIGR and MIPs contain information just as was shown for Arabidopsis The Orygenes and Gramene buttons are new…

22. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families OryGenes is a site sponsored by Cirad and is similar to SALK for Arabidopsis For each gene, any available insertion lines are shown with their location in the gene OryGenes uses the same genome browser (GBrowse) that many sites, including SALK make use of to display information

23. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families The Gramene button links to Gramene.org at the location of that particular rice gene Gramene contains a wealth of cereal synteny data including gene model, sequence, marker, and EST alignments for many cereals such as rice, maize, wheat, barley, and oat

24. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families As with the Arabidopsis tree, you can click on the Maize tree to bring up an interactive FLASH file of a radial dendrogram of the gene family members Clicking on the individual clades brings up a closer view such as AUD/SUD- like…

25. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families Clicking on the AUD/SUD clade opens a close-up view of the genes as a radial dendrogram There are no clickable links yet but we hope to add some similar to the rice links later The blue text indicates gene fragments while green text is full sequence

26. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: CWG Families The combined dendrogram link takes you to a square dendrogram of Arabidopsis, rice, and maize families (part of 1.1 is shown) The red names are Arabidopsis sequence, the black names are rice, and the green names are maize Regions alternate between grey shaded and white backgrounds to indicate clades (such as AUD/SUD or GME genes, etc)

27. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: Techniques The techniques page has links to descriptions of many of the procedures we use to gather our data and that are useful to cell wall biologists

28. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: Web Links The web links page lists sites with information used in the construction of our site and useful to cell wall biologists After each link is a short description of what can be found at the site

29. Supported by the NSF Plant Genome Research and REU Programs Site Tutorial: Contacts The contacts page lists contact information for a number of our group members to which you can provide site feedback For more information on trees, FTIR, or the website you can also contact Bryan Penning: bpenning@purdue.edu

30. Supported by the NSF Plant Genome Research and REU Programs Websites shown in this tutorial Cell Wall genomics: http://cellwall.genomics.purdue.edu/http://cellwall.genomics.purdue.edu/ Oligogo: http://oligogo.botany.wisc.edu/http://oligogo.botany.wisc.edu/ UniformMu: http://currant.hos.ufl.edu/mutail/Cell_Wall_Gene_Knockouts.html http://currant.hos.ufl.edu/mutail/Cell_Wall_Gene_Knockouts.html TIGR: http://www.tigr.org/http://www.tigr.org/ MIPS: http://mips.gsf.de/http://mips.gsf.de/ TAIR: http://arabidopsis.org/http://arabidopsis.org/ SIGnAL: http://signal.salk.edu/http://signal.salk.edu/ OryGenes: http://orygenesdb.cines.fr/http://orygenesdb.cines.fr/ Gramene: http://www.gramene.org/http://www.gramene.org/