Identification of genes differentially expressed in 1 dpa and 10 dpa fiber

A method was developed to isolate RNA from 1 dpa fiber. ESTs derived from this and other cotton mRNAs were sequenced and assembled into contigs. Contigs composed of EST unique to libraries of interest and unique singletons were represented on a microarray. Microarrays were hybridized with labed nucleic acids derived from 10 dpa fiber and 1 dpa fiber to identify genes differentially regulated during fiber initiation and fiber elongation. Genes with known expression in fiber were included to validate the microarray. Analysis of the gene ontology (GO) of differentially expressed genes suported previously reported aspects of fiber initiation such as cell wall remodeling. Transcription factors upregulated in fiber initials and elongating fiber were identified Keywords: cell type comparison Overall design: The microarray represents 11143 gene models. One gene model is represented by 5 different oligonucleotides, 8604 gene models are represented by 4 different oligos, 1706 gene models are represented by 3 different oligonucleotides, 831 gene models are represented by 3 of the same oligonucleotides and one gene model is represented by 2 different oligonucleotides. Each micro array is hybridized with a labeled nucleic acid derived form RNA isolated from 1 dpa fiber or 10 dpa fiber harvested on different days from field grown plants. One is a dye swap.