94 k brassica napus microarray dataset  (CombiMatrix)

Journal: PLoS ONE

Article Title: Identification of Heat Responsive Genes in Brassica napus Siliques at the Seed-Filling Stage through Transcriptional Profiling

doi: 10.1371/journal.pone.0101914

Figure Lengend Snippet: Relative expression levels of 18 up-regulated genes were detected in the SW and seeds sampled at 24 h (A and B) and 48 h (C and D) after heat treatment. 10 down-regulated genes, of which 5 involving glucosinolate metabolism and another 5 associated with flavonoid synthesis were analyzed in the SW (E) and seeds (F) at 24 h after treatment respectively. Two genes may responsible for lipid synthesis were also detected in seeds (G). (H) Correlation of the gene expression ratios obtained from qRT-PCR and microarray data. The qRT-PCR log 2 value of the expression ratio (y-axis) has been plotted against the value from the microarray (x-axis). The results of all the tested genes were listed in detail in . Data were collected from three biological replicates and three technical replicates for each sample.

Article Snippet: Total RNA was extracted using a cetyltrimethylammonium bromide extraction method and assessed by spectrophotometry and bioanalysis before proceeding to analysis with the Agilent Brassica 95k EST Microarray , developed by the John Innes Centre in collaboration with JCVI (J. Craig Venter Institute) and Cogenics. cDNA synthesis, labeling, hybridization, washing, scanning and data extraction were performed using established procedures for the analysis of eukaryotic RNA by the Cogenics Microarray Core Facility (Morrisville, NC, US).

Techniques: Expressing, Quantitative RT-PCR, Microarray

Journal: BMC Plant Biology

Article Title: Analysis of ambient temperature-responsive transcriptome in shoot apical meristem of heat-tolerant and heat-sensitive broccoli inbred lines during floral head formation

doi: 10.1186/s12870-018-1613-x

Figure Lengend Snippet: Distribution and functional classification of the differentially expressed genes. a Venn diagram showing the number of upregulated genes (numbers in black) in the HT genotype and the upregulated (numbers in blue) in the HS genotypes at 15 °C, 22 °C, and 27 °C. Results were based on the FDR < 0.05 and two-fold change in expression. b Gene Ontology analysis of the significantly temperature-associated genes (fold change ≥2) by microarray analysis. The agriGO database was used to perform enrichment analysis and the negative log of the P value is shown for the significantly enriched gene categories. c MapMan analysis of the secondary metabolism-associated genes. Each gene displayed as a square, red for upregulation and blue for downregulation. d The relative expression of probes assigned as epithiospecifier protein (ESP) and branched-chain aminotransferase4 (BCAT4) at 15 °C, 22 °C, and 27 °C in the HT and HS genotypes

Article Snippet: To reveal the difference in the signaling pathway between the HT and HS genotypes under different temperatures (15 °C, 22 °C, and 27 °C), we performed microarray analysis of shoot meristems from the HT and HS genotypes by using the Brassica napus microarray chip (Agilent, Cat. No. G2519F-022520).

Techniques: Functional Assay, Expressing, Microarray

Journal: Frontiers in Plant Science

Article Title: Recent progress in the use of ‘omics technologies in brassicaceous vegetables

doi: 10.3389/fpls.2015.00244

Figure Lengend Snippet: Published transcriptomic analyses in the brassicaceous vegetables.

Article Snippet: With the recent acquisition of Brassica spp. genome sequences, a number of Brassica -specific microarrays are finally becoming available – these include the B. rapa 24 K oligo microarray and the Agilent Brassica microarray, which is able to detect the transcription of >27,000 unigenes in a range of Brassica spp.

Techniques: Sterility, Microarray