microarray suite (mas) 5.0 software  (Thermo Fisher)

Journal: Genome Biology

Article Title: Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte

doi: 10.1186/gb-2007-8-10-r204

Figure Lengend Snippet: A genetic subtraction strategy for determination of the embryo sac transcriptome. (a) A branch of a coatlique ( coa ) showing undeveloped siliques. Arrows point to a small silique, which bears female sterile ovules inside the carpel (insert: wild-type L er branch). (b) Morphology of a mature wild-type ovule bearing an embryo sac (ES) before anthesis. (c) A functional embryo sac is absent in coa (degenerated megaspores [DM]). Note that the ovule sporophyte is morphologically equivalent to that of the wild type. (d) Functional categories of genes identified by a microarray-based comparison of coa and sporocyteless ( spl ; based on data from Yu and coworkers [34]) with the wild type. The embryo sac expressed transcriptome is shown to the left. Embryo sac expressed genes were grouped as preferentially expressed in the embryo sac if they were not detected in previous sporophytic microarrays [28]. The size of the specific transcriptome in each class is marked on each bar by a dark outline. Functional categories of genes that were identified as over-expressed in the sporophyte of coa and spl are shown to the right. Scale bars: 1 cm in panel a (2 cm in the insert of panel a), and 50 μm in panels b and c.

Article Snippet: We used the following three methods in data analyses: the microarray suite software (MAS; Affymetrix) and Genspring; the DNA Chip analyzer (dCHIP) package [ ]; and GC robust multi-array average analysis (gcRMA) [ ].

Techniques: Functional Assay, Microarray

Journal: Genome Biology

Article Title: Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte

doi: 10.1186/gb-2007-8-10-r204

Figure Lengend Snippet: Gain of expression in the sporophyte in the absence of a functional embryo sac: expression analysis in the coatlique ( coa ) mutant. (a) RT-PCR for 11 genes in coa and wild-type (WT) pistils. Equal loading of both coa and WT cDNA templates in PCR was monitored by expression of ACT11 . SUP , SUPERMAN . Also shown are in situ expression patterns of the following genes in coa pistil tissues: (b) AT4G12410 , encoding an auxin-responsive Small Auxin Up RNA (SAUR) protein; (c) AT1G75580 , encoding an auxin-responsive protein; (d) AT5G03200 , encoding a C3HC4-type RING finger protein; and (e) at5g15980, encoding a PPR repeat containing protein. The corresponding sense control probes did not show any expression (data not shown). (f) AT4G12410 did not show any detectable expression pattern in wild-type pistils. The other four genes exhibited spatial expression patterns in the wild-type ovule and carpel tissues comparable to that of coa , but their wild-type expression levels were much lower than in coa (data not shown). (g) We initially identified the over-expression of STM in the ovule tissues of spl ( sensu microarray data), and confirmed that this gene is over-expressed in the carpel and ovules of coa as well (panels a and g). (h) A comparable but less intense spatial expression pattern of STM was seen in wild-type pistils. Scale bars: 100 μm in panels b to h.

Article Snippet: We used the following three methods in data analyses: the microarray suite software (MAS; Affymetrix) and Genspring; the DNA Chip analyzer (dCHIP) package [ ]; and GC robust multi-array average analysis (gcRMA) [ ].

Techniques: Expressing, Functional Assay, Mutagenesis, Reverse Transcription Polymerase Chain Reaction, In Situ, Over Expression, Microarray