Additional file 3: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

Normalized transcript expression counts for WT and cngc16 pollen with and without HS. Expression counts from Additional file 2 were subjected to exclusions/filters and normalized as described in methods. Expression data from other transcriptome studies (microarray and RNA-Seq) were added to the table for comparisons. These included an RNA-Seq data set for WT pollen and seedlings from Loraine et al. 2013 (PMCID: PMC3668042 [22]), two pollen microarray experiments from Qin et al. 2009 (PMCID: PMC2726614 [23]) and Borges et al. 2008 (PMCID: PMC2556834 [72]), and finally HS seedlings from Schmid et al. 2005 (PMID:15806101 [33]), respectively. Ratios of expression between pollen and seedling are based on Loraine et al. 2013 (PMCID: PMC3668042 [22]). In cases where the seedling value was below the limit of detection, a minimal value of 0.0019 was substituted in its place as a denominator (0.0019 was the RPKM for ATCG00860 and was the lowest value reported in Loraine et al. 2013 (PMCID: PMC3668042 [22]). Ratio of expression between semi-in vivo pollen tube over dry pollen is based on Qin et al. 2009 (PMCID: PMC2726614 [23]). HS dependent changes in transcript abundance in shoots were based on publicly available data using the AtGenExpress Visualization Tool (AVT) ( http://jsp.weigelworld.org/expviz/expviz.jsp , Schmid et al. 2005 (PMID:15806101 [33] for seedlings exposed to one hour HS at 38 °C). The log2-fold change was calculated based on a comparison of means of normalized values for two heat-stressed and two non-stressed seedling samples. NA stands for not available. Not Calculated, refers to a value not being calculated because one of the input sample read counts was considered to have an extreme outlier (see AT2G42540 and ATMG01360). (XLSX 8952 kb)