Information on previous array versions

• v1.0 Array Info Spreadsheet [for Excel]
• v1.0 "SMD GalFile" (gives clone IDs by block, row, and column)

• v1.1 FAQ
• Search for genes by (approximate) annotation among the sequences on the array.
• v1.1 Array Info Spreadsheet [for Excel] [as a tab-separated values (tsv) file].
• Stanford Microarray Database layout files (print #871):
     "Godlist"
     GenePix "Gal" File
     Spot list
     Plate order
  

Version 2 Microarray Is Now Available

This array consists of about 10,000 oligonucleotides, each approximately 70 nucleotides long. You can download an Excel file that gives all the sequences. Each of the oligonucleotides should represent a unique gene. The set of 10,000 oligonucleotides was printed twice on the same slide (so each slide has duplicates). The oligonucleotides were prepared by Integrated DNA Technologies and their quality was checked by mass spectroscopy. The set of 'unigenes sequences' used for oligonucleotide generation was developed by Monica Jain and Stephan Eberhard in my laboratory. We will also provide information describing potentially empty and weak spots (there were very few of these in our initial examination). While the .gal file with a gene identifier and the sequence of the oligonucleotide used at each position on the array will be available, it may take a little more time to link whatever annotation is available to the individual spots (it will be a priority over the next month or two). We will also put a protocol onto the web site that we used for the hybridizations and will try to address any technical questions that you might have concerning the array. A manuscript describing how the unigene set was chosen and oligonucleotide design is in preparation, and we will make it available to people using the array as soon as possible.

The cost is $100 per slide. Please send orders to:

Arthur Grossman
Department of Plant Biology
Carnegie Institution of Washington
260 Panama Street
Stanford, CA 94305
Email: arthurg@stanford.edu
Telephone: 650 325-1521 X 212

If you have any questions contact me by Email or phone.

Cheers,
Arthur

protocol for using the array [MS Word file, revised version posted July 28, 2005; thanks to Stephan Eberhard! ]

details of selection of ACEGs for preparation of oligos [PowerPoint file; also thanks to Stephan Eberhard!]

gal file [tab-delimited text file, can be opened in Excel; revised version posted July 28, 2005]
The galfile describes the array. It is typically loaded into a program like GenePix. Two additional columns have been added which describe the user-curated and automatic annotations given to each gene (if either such annotations exist). Depending upon what exact programs you are loading the file into, you may have to make format changes that are specific to that program, for example, adding blank columns. See the user's guide for your specific program to figure out what changes are needed.

(Image: Zhaoduo Zhang; Conditions: sulfur stress, wild type v. sac1 mutant, 4hrs.)