A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors-0

<p><b>Copyright information:</b></p><p>Taken from "A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors"</p><p>http://www.plantmethods.com/content/3/1/7</p><p>Plant Methods 2007;3():7-7.</p><p>Published online 8 Jun 2007</p><p>PMCID:PMC1914063.</p><p></p>DNA (gDNA), evaluation of cDNA quality, primer design and data analysis. The absence of gDNA was confirmed by quantitative RT-PCR (qRT-PCR) with primer pairs targeting various non-coding regions. The quality of the cDNA was tested using different reference genes, as outlined in the text

A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors-1

<p><b>Copyright information:</b></p><p>Taken from "A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors"</p><p>http://www.plantmethods.com/content/3/1/7</p><p>Plant Methods 2007;3():7-7.</p><p>Published online 8 Jun 2007</p><p>PMCID:PMC1914063.</p><p></p>erent at p = 0.001. Non-parametric comparison of mean values (Mann-Whitney U test) confirmed the presence of statistically significant differences at p = 0.000001. Transformation to expression values revealed that the slightly different PCR efficiencies could lead to a mean difference of maximal 0.3, when the fold change was expressed as log. Individual primer pairs can thus exhibit slight differences for their target genes in different cultivars. However, this does not significantly affect the overall applicability of the primer platform for expression profiling experiments (Caldana ., manuscript in preparation)

A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors-2

<p><b>Copyright information:</b></p><p>Taken from "A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors"</p><p>http://www.plantmethods.com/content/3/1/7</p><p>Plant Methods 2007;3():7-7.</p><p>Published online 8 Jun 2007</p><p>PMCID:PMC1914063.</p><p></p> ng) and used as template to test transcript abundance of three selected genes (Os03g55610, Os08g38220, and Os12g38200) via qRT-PCR. A linear relationship between root (or shoot) cDNA and expression level of the various genes was observed. Symbols in both panels represent the mean ± SD (= 3)

Additional file 2: of Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Table S1. List of genes represented in Rice TF Primer Platform (Caldana et al., 2007). Complete list of 2508 TF genes, their primer sequences and their corresponding PCR efficiencies. Genes were presented with version 2.0 and version 5.0 RGAP genome annotations. Table S2. Transcription factor genes with and without annotations in version 5.0 and 7.0 of RGAP Pseudomolecule. Table S3. Expression profile of transcription factor genes in IR64 control and stress-treated plants upon submergence. Recorded Ct, R2, Efficiency and ΔCt values for all reactions. The list of used reference genes and their distribution on the plates is also given. Table S4. Expression profile of transcription factor genes in IR64-Sub1 control and stress-treated plants upon submergence. Worksheets record Ct, R2, Efficiency and ΔCt values for all reactions. The list of used reference genes and their distribution on the plates is also given. Table S5. Promoter sequences of SUB1A-1 and SUB1A-2. Table S6. Moderated t-tests results from LIMMA package for identifying differentially expressed genes. P-values were recorded and FDR corrections were also performed. Table S7. Details about the list of differentially expressed genes and their putative functions. (DOCX 29 kb

Additional file 1: Figure S1. of Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

The submergence tolerance locus Sub1 in rice. The Sub1 locus is located on rice chromosome 9 with a variable number of SUB1 genes. In different rice genotypes, SUB1A is either absent or present as different allele. (a). Introgression of the Sub1 locus into the rice variety IR64 (IR64-Sub1) enhanced survival after complete submergence. (b). The photo shows the IRRI demonstration field plot in the Philippines. Phenotyping for submergence tolerance can also be conducted by submerging plants grown in trays (inlay). The SUB1A-1 and SUB1A-2 alleles are both highly expressed in nodes of submerged plants but SUB1A-1 expression is higher in internodes. (c). Schematic illustration based on (Singh et al., 2010). (PPTX 3066 kb

Additional file 3; Figure S2. of Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice

Sequence alignment of the SUB1A-1 and SUB1A-2 upstream promoter regions. 2 kb upstream of the start site (promoter regions) were analysed for SUB1A-1 and SUB1A-2 alleles and putative cis-regulatory elements were identified. (XLSX 3.76 kb