• Fig1_smalldraft.jpg
  • Fig2_smalldraft.jpg
  • Fig3_smalldraft.jpg
  • Fig4_smalldraft.jpg

Instructions for performing RMA analyses using Partek Genomics Suite

1.When using the axolotl array you will need to download the Library files for the corresponding genechip from here. Make sure they are unzipped and saved in a folder that Partek can access.

2.Open Partek Genomics suite.

3.Select File->Import->Affymetrix->CEL files

4.Select the .CEL files that correspond with chips in the current study.

5.Select Use RMA

6.Click Import

7.The first time this is done, the program may ask to specify a library folder, select the folder that has the .CDF and .CLF files.

8.The data should open as a spreadsheet in Partek. Partek is capable of further downstream analyses. Each row should be one chip. Many useful tools can be found in the “View” and “Stats” tabs. The Gene Expression Workflow may also be veryWithin the Gene Expression workflow is an “Add Sample Attributes” option which will allow the chips to be sorted into experimental groups for statistical analyses.

Instructions for performing RMA analyses in Expression console

1. The RAW data should come as Affymetrix .CEL files. Save the files and remember their location.

2.Go to www.affymetrix.com If you don’t have an account click “register” and create an account. Otherwise, log in.

3.Use the search tool to look up Affymetrix Expression Console. (The software used to be free and readily downloadable from Affymetrix. It appears you have to inquire about it now.)

4.When you first start the software, you should be asked which folder the program should look for library files in. Specify a folder and make sure you save library files into that folder.

5.When not using the axolotl array, the download library files and download annotation files options under the “File” tab will allow you to readily download files.

6.When using the axolotl array you will need to download the Library files for the corresponding genechip from here. Make sure they are unzipped and saved in the folder that Expression Console searches for library files.

7.Select File->New study

8.A box should appear. In that box, click “Add Intensity Files”

9.Select all the .CEL files that are associated with chips that are part of the study.

10.The file names of those CEL files should be added inside the box.

11.Make sure all the CEL files are checked.

12.Select Analysis->3’ Expression Arrays->RMA

13.After running the analysis, a new list of files should be created, listed in the box, and checked. These are .CHP files and represent the normalized data.

14.Click “Uncheck all” and then click “Check Group” and select “RMA-Group 1”, the .CHP files should all be selected.

15.Select Export->Export Probe Set Results (pivot table)to Txt

16.This will open a save prompt. Save your results as a .txt file.

17.The new .txt file can be opened in Excel. This file is the normalized data and should be ready for analysis.

Salamanders in Research
Salamanders have served as model organisms for more than a century. A majority of the earliest embryological and morphological analyses of vertebrate development were conducted using salamander embryos. Today, salamanders continue to be the best animal models for several areas of research and a new generation of researchers are adopting salamanders – and in particular the Mexican axolotl - as their primary animal model. This webpage provides links to projects that are developing resources to enhance the salamander models.

Join the Salamander Research Network

 A Slack Workspace has been setup to facilitate communication about all things salamander, please join!

 

Ambystoma Community:

People Area of Research
Melissa Gibbs, Ph.D.  
Stetson University  
Assistant Professor Education
Director, Aquatic and Marine Biology Program  
(386) 822-8172  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
David Shook, Ph.D.  
University of Virginia Research
Research Scientist (morphogenesis)
434 243 2596 (lab)  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Julie Drawbridge, Ph.D.  
Rider University Education & Research
Professor (cell migration during pronephric organogenesis)
609-895-5428  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Bernd Fritzsch, Ph.D.; Fellow AAAS  
University of Iowa  
DEO, Department of Biology Research
319-353-2969 (genomic expression analysis)
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Spencer M. Mass, MD  
SUNY New Paltz Education & Research
Developmental Biology Laboratory (xenoestrogen embryo toxicology and regeneration research)
845-257-3678  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Stéphane Roy, Ph.D.  
Université de Montréal Research
Associate Professor, Faculty of Dentistry (molecular mechanisms regulating limb regeneration)
514-343-6111 ext 1780  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Craig Crews, Ph.D.  
Yale University Research
Molecular, Cellular & Developmental Biology (importance of the regenerating epidermis during limb regeneration)
203-432-9364  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Heather Eisthen  
Michigan State University Research
Department of Zoology (neurobiology and behavior)
517-353-1953   
www.msu.edu/~eisthen/lab  
   
Ellen Chernoff, Ph.D.  
IUPUI Research
Developmental Biology (spinal cord and limb regeneration)
317-274-0591  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Brian C. Ring, Ph.D.  
Valdosta State University  
Associate Professor Education
229-249-4841  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Frank W. Grasso, Ph.D.  
Brooklyn College, CUNY Education & Research
Associate Professor (undergraduate students conduct behavioral experiments)
718-951-5000 x 6020  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Richard Gordon, Ph.D.  
University of Manitoba Research
Professor (Google Embryo)
(204) 789-3828  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Michelle L. McWhorter, Ph.D.  
Wittenberg University Education
Assistant Professor  
937-327-6483  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Chester R. Figiel, Jr., PhD  
U.S. Fish and Wildlife Service Research
Warm Springs Fish Technology Center (cryopreservation of sperm for Ambystoma salamanders)
Supervisory Fish Biologist  
706-655-3382 ext. 1244  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Ralph A. Sorensen, Ph.D.  
Gettysburg College Education
Professor  
717-337 – 6168  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Moshe Khurgel, Ph.D.  
Bridgewater College Education & Research
Assistant Professor  
540-515-3767  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
James N. MacLeod, VMD, Ph.D.  
University of Kentucky  
Gluck Equine Research Center Research
Department of Veterinary Science (joint development and articular cartilage repair questions)
859- 218-1099  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
William H. Donahue, Ph.D.  
St. John's College, Santa Fe  
Director of Laboratories Education
505-984-6452  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Thomas Diekwisch, D.M.D., Ph.D.  
UIC College of Dentistry  
Professor& Head, Dept. of Oral Biology Research
Director, Brodie Lab for Craniofacial Genetics (tooth development)
Allan G. Brodie Endowed Chair for Orthodontic Research  
312-413-9683  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Jonathan Slack, Ph.D.  
University of Minnesota Education & Research
Stem Cell Institute  
612-625-0602  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Andrew Johnson, Ph.D.  
University of Nottingham  
Associate Professor Research
Faculty of Medicine & Health Sciences (early development and identify conserved developmental pathways)
+44 0115 8230366  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Panagiotis A. Tsonis, Ph.D.  
University of Dayton  
Professor Research
Director, Center for Tissue Regeneration and Engineering at Dayton (TREND)  
937-229-2579  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
James Hanken, Ph.D.  
Harvard University Research
Dept. of Organismic & Evolutionary Biology (craniofacial developmental biology and evolution; map embryonic origins of the bony skull and shoulder girdle)
Professor  
Director, Museum of Comparative Zoology  
617-495-2496  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Jessica Bolker, Ph.D.  
University of New Hampshire Education
Department of Biological Sciences  
Associate Director, Shoals Marine Laboratory 603-862-0071  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Malcolm Maden, Ph.D.  
University of Florida  
Professor Research
Dept. of Biology & UF Genetics Institute (the controls of limb regeneration, skin regeneration, spinal cord regeneration and brain regeneration)
352-392-5856 or 352-273-7875  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Katia Del Rio-Tsonis, Ph.D.  
Miami University Education
Professor  
513-529-3128  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Tim Walston, Ph.D.  
Truman State University Research
Assistant Professor of Biology  
660-785-4017  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Thomas Akre, Ph.D.  
Longwood University  
Associate Professor Education
Biological and Environmental Sciences  
434-395-2731  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Kathryn Malody  
Hamline University  
Lab Manager & Instructor Education
651-523-3026  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Robin Ikeda, Ph.D.  
Chaffey College  
Professor, Biology Education
909-652-6420  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Brian Hyatt, Ph.D.  
Bethel University  
Co-chair, Dept. of Biological Sciences Education
Associate Professor  
651-638-6802  
This email address is being protected from spambots. You need JavaScript enabled to view it.  
   
Erick Garcia Diaz de la Vega  
Universidad Nacional Autonoma de Mexico Education & Research
(5255) 46-09-03-82  

 

Fun Facts

Why do axolotls retain a juvenile appearance throughout life?

Several salamanders, including the axolotl, retain juvenile characteristics as adults and are called paedomorphic.

The entire axolotl life cycle is spent under water, from birth to mating.

Read more ...