Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression profiling of cotton (Gossypium barbadense L. Pima S7) fiber transcriptome during the development

ABSTRACT: To gain novel insights into the molecular mechanisms underlying Pima cotton fiber quality, expression profiling of the Pima fiber transcriptome was performed as a function of development. The profiling was performed at 6 developmental time points: 8, 11, 14, 17, 21, and 24dpa. The expression profiling using long oligonucleotide microarray showed dynamic changes to the fiber transcriptome that correlate to morphogenesis, and biological cellular processes. Differentially expressed genes were identified by being differentially regulated at various stages of fiber development, and they were used to develop stage-specific regulation patterns that correlate the dynamics of gene expression to fiber morphogenesis. A bi-directional double loop hybridization (Kerr and Churchill, 2001) with dye swap experimental design encompassing a total of 28 hybridizations was employed to maximize discovery of significant changes between developmental stages. Self-hybridization controls were conducted to evaluate both within-array correlation and dye bias.

ORGANISM(S): Gossypium barbadense

SUBMITTER: Bulak Arpat

PROVIDER: E-GEOD-11689 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Double feature selection and cluster analyses in mining of microarray data from cotton.

Alabady Magdy S MS Youn Eunseog E Wilkins Thea A TA

BMC genomics 20080620

<h4>Background</h4>Cotton fiber is a single-celled seed trichome of major biological and economic importance. In recent years, genomic approaches such as microarray-based expression profiling were used to study fiber growth and development to understand the developmental mechanisms of fiber at the molecular level. The vast volume of microarray expression data generated requires a sophisticated means of data mining in order to extract novel information that addresses fundamental questions of biol ...[more]

PMID: 18570655

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Project description:MM-CM-<ller cells are the principal glial cells in the retina. Alterations in MM-CM-<ller cell behaviour are observed in retinal tissue from patients with proliferative diabetic retinopathy. The purpose of this study was to compare gene and protein expression profile of normal human MM-CM-<ller cells (NHMC) with two spontaneously human MM-CM-<ller cell lines generated from type 1 (HMCL-I) and type 2 (HMCL-II) diabetic donors using Serial Analysis Gene Expression (SAGE). Approximatively 50 000 tags were sequenced for each of the three SAGE libraries. Identification of the transcripts was obtained by matching the 15bp (CATG + 11bp) with the UniGene and GenBank databases. Classification of the genes was based upon the updated information of the genome directory found at the NCBI website. SAGE allowed us to characterize the entire transcriptome of human MM-CM-<ller cells and to compare these data with those from MM-CM-<ller cells of type 1 and 2 diabetic donors. Polyadenylated RNA was extracted with the Oligotex mRNA Purification System (Qiagen), annealed with the biotin-5 -T18-3 primer and converted to cDNA with the cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA). The resulting cDNA library was digested with NlaIII (anchoring enzyme), and the 3M-bM-^@M-^Y restriction fragments were isolated with streptavidin-coated magnetic beads (Dynal Biotech, Oslo, Norway) and separated into two populations. Each population was ligated to one of the two annealed linker pairs and extensively washed to remove unligated linkers. The tag beside the most 3M-bM-^@M-^Y NlaIII restriction site (CATG) of each transcript was released by digestion with BsmFI (tagging enzyme). The blunting kit from Takara Co. (Otsu, Japan) was used for the blunting and ligation of the two tag populations. The resulting ligation products containing the ditags were amplified by PCR with an initial denaturation step of 1 min at 950C, followed by 22 cycles of 20 s at 940C, 20 s at 600C and 2 s at 720C with 27 bp primers. The PCR product was digested with NlaIII, and the band containing the ditags was extracted from the acrylamide gel. The purified ditags were self-ligated to form concatemers. The concatemers of 500 to 1800bp were isolated by agarose gel. The resulting DNA fragments were ligated into the SphI site of pUC19 and cloned into UltraMAX DH5M-oM-^AM-!FT (Invitrogen). White colonies were screened by PCR to select long inserts for automated sequencing. Sequence files were analyzed by the SAGEana program, a modification of SAGEparser (ftp://ftp.pbrc.edu/public/eesnyder/SAGE/). Tags corresponding to linker sequences were discarded, and duplicate concatemers were counted only once. We used the comparative count display (CCD) test to identify the transcripts that were differentially expressed significantly (P<0.05) between the groups with more than a twofold change. The CCD test makes a key-by-key comparison of two key-count distributions by generating a probability that the frequency of any key in the distribution differs by more than a given fold factor from the other distribution.

Dataset Information

Expression profiling of cotton (Gossypium barbadense L. Pima S7) fiber transcriptome during the development

Publications

Double feature selection and cluster analyses in mining of microarray data from cotton.

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