affy_cotton_2011_12 - Comparative transcriptional profiling of cotton fibers in Gossypium hirsutum and Gossypium barbadense using EST pyrosequencing and microarray hybridization. affy_cotton_2011_12 - Comparative transcriptional profiling of cotton fibers in Gossypium hirsutum and Gossypium barbade

affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). - Overall design: 4 arrays - Cotton; x comparison between two genotypes in cell type This represents the gene expression component of the study only

affy_cotton_2011_12数据集——本研究针对陆地棉（Gossypium hirsutum）与海岛棉（Gossypium barbadense）两个棉属物种的纤维转录组展开系统表征，二者均为此前用于表型数量性状位点（Quantitative Trait Locus, QTL）与表达数量性状位点（expression QTL, eQTL）作图的重组自交系（Recombinant Inbred Line, RIL）作图群体的亲本基因型。
本研究采用454深度焦磷酸测序技术，对开花后10天与22天（days post anthesis, dpa）两个关键发育时期的发育纤维互补DNA（complementary DNA, cDNA）进行测序表征。我们组装并注释了单基因集（unigene set），并通过组装重叠群（contigs）中不同发育时期与基因型的读段丰度，评估了数字化差异基因表达模式。作为补充分析策略，我们使用棉花Affymetrix基因芯片开展基于微阵列的杂交表达谱分析，对开花后11天（11 dpa）的纤维cDNA进行标记检测，采用与前述一致的两个棉属基因型，并对两个测序平台鉴定出的差异表达基因进行了比较。此外，我们还对454测序得到的单基因集进行了挖掘，筛选出可用于棉花遗传作图与标记辅助选择育种的微卫星重复序列与单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）分子标记。
我们从两个基因型——瓜春2号（Guazuncho 2，陆地棉）与VH8-4602（海岛棉）——的11 dpa纤维中提取了总RNA，每个基因型设置两个生物学重复。参照制造商操作指南，我们使用安捷伦生物分析仪2100（Agilent Bioanalyser 2100，安捷伦科技公司，美国加利福尼亚州圣克拉拉市，http://www.home.agilent.com）对RNA的质量与浓度进行了质控检测。随后，将RNA样本送至澳大利亚基因组研究中心有限公司（Australian Genome Research Facility Ltd.，澳大利亚维多利亚州墨尔本，http://www.agrf.org.au）进行标记，并与Affymetrix Cotton Genome Array基因芯片（包含21854个基因）进行杂交（Affymetrix，http://www.affymetrix.com/）。
实验整体设计：共设置4张棉花基因芯片，用于比较两种基因型在特定细胞类型中的基因表达差异，本部分仅涵盖研究中的基因表达相关组分。