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Cotton Oligonucloetide Microarray

     
 

News: Advances in RNA-seq technologies are supplanting microarrays for expression analysis and demand for our Cotton array has diminished. Therefore, we are no longer offering Cotton Oligonucleotide Microarrays.

Overview

         An update version of the Cotton Oligonucleotide Microarray (v2) has been released. The original Cotton Oligonucleotide Microarray (v1) was composed of 12,006 IDT oligonucleotides derived from an assembly of more than 180,000 Gossypium ESTs sequenced from 30 cDNA libraries. Subsequently, approximately 9,000 additional oligonucleotide probes have been designed bringing the total number of oligonucleotide probes to approximately 21,000. Sequences from fifty-two cDNA libraries were collected from 14 different research groups across the globe. These libraries were constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges, and represents allopolyploid cotton as well as its two diploid progenitors. Most cDNA libraries (28) were derived from G. hirsutum and were relatively small (from 576 to 8,643 ESTs) with one exception. The ovule cDNA library from TM-1 cultivar was recently created and 32,789 new ESTs sequences were generated. Collectively, these G. hirsutum EST collections comprised 64% of the total used in the assembly. The remaining ESTs were derived from three deeply sampled cDNA libraries generated from the two diploids (one library from 7-10 dpa fiber of G. arboreum and two libraries of G. raimondii), comprising 15% and 23% of the total number of ESTs, respectively. The G. arboreum fiber library was normalized to remove highly redundant transcripts (Arpat et al., 2004), while the G. raimondii cDNA libraries were not normalized because their redundancy was so low, perhaps due to the heterogeneous tissue sources used for RNA isolation (whole flowers and whole seedlings). To browse or query the ESTs that make up these libraries, go to PAVE in the EST libraries section of the website.

         Development of this microarray was funded as part of two separate Plant Genome Program awards from two separate National Science Foundation awards with Jonathan Wendel and Z. Jeffery Chen as the Principle Investigators, respectively. The microarrays were printed at the University of Washington's core facility on Corning epoxy slides. As noted above, advances in RNA-seq technologies are supplanting microarrays for expression analysis and demand for our Cotton array has diminished. Therefore, we are no longer offering Cotton Oligonucleotide Microarrays.

The Cotton Oligonucleotide Microarray (v2) GAL file is available for download.

Please note that we have recently (5/10/2007) updated our probe Ids, adding a unique number identifier as the primary Id. The gal file has been updated as well. This has been done as an aid to tracking related Ids as sequence assemblies are updated.

An Id conversion table is also available.


We welcome your comments and suggestions.