*Supported by the NSF Plant Genome Research and REU Programs

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

2. 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. 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. 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. 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. 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. 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. 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. 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. 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/) • 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. 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.purdue.edu/

12. 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.genomics.purdue.edu/techniques/8.html

13. 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. 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/ • Each oval can be clicked to open a close up view of the individual clade, such as AUD/SUD (next page)…

15. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Websites shown in this tutorial • Cell Wall genomics: http://cellwall.genomics.purdue.edu/ • Oligogo: http://oligogo.botany.wisc.edu/ • UniformMu: http://currant.hos.ufl.edu/mutail/Cell_Wall_Gene_Knockouts.html • TIGR: http://www.tigr.org/ • MIPS: http://mips.gsf.de/ • TAIR: http://arabidopsis.org/ • SIGnAL: http://signal.salk.edu/ • OryGenes: http://orygenesdb.cines.fr/ • Gramene: http://www.gramene.org/