Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.
Project description:The differentiation of specialized feeding sites in Zea mays root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Zea mays root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation. Overall design: Each time point (14 day and 21 day) consisted of three biological replicates per treatment (control root cells or giant cells). Control cells were captured from an area ~13,000,000 um2 in size and giant cells were captured from an area ~5,000,000 um2 in size. RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA amplifications were carried out with the NuGEN WT-Ovation Pico kit.
Project description:Whole Genome Metabolism of "Zea mays"
This is a whole genome metabolism model of Zea mays.
This model has been automatically generated by the SuBliMinaL Toolbox
and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).
This model has been produced by the path2models
project and is currently hosted on BioModels Database
and identified by: BMID000000140835
Other models with the same genus include BMID000000025302 BMID000000025303 BMID000000025304 BMID000000025305 BMID000000025306 BMID000000025307 BMID000000025308 BMID000000025309 BMID000000025310 BMID000000025311 BMID000000025312 BMID000000025313 BMID000000025314 BMID000000025315 BMID000000025316 BMID000000025317 BMID000000025318 BMID000000025319 BMID000000025320 BMID000000025321 BMID000000025322 BMID000000025323 BMID000000025324 BMID000000025325 BMID000000025326 BMID000000025327 BMID000000025328 BMID000000025329 BMID000000025330 BMID000000025331 BMID000000132155 BMID000000132156 BMID000000132157 BMID000000132158 BMID000000132159 BMID000000132160 BMID000000132161 BMID000000132162 BMID000000132163 BMID000000132164 BMID000000132165 BMID000000132166 BMID000000132167 BMID000000132168 BMID000000132169 BMID000000132170 BMID000000132171 BMID000000132172 BMID000000132173 BMID000000132174 BMID000000132175 BMID000000132176 BMID000000132177 BMID000000132178 BMID000000132179 BMID000000132180 BMID000000132181 BMID000000132182 BMID000000132183 BMID000000132184 BMID000000132185 BMID000000132186 BMID000000132187 BMID000000132188 BMID000000132189 BMID000000132190 BMID000000132191 BMID000000132192 BMID000000132193 BMID000000132194 BMID000000132195 BMID000000132196 BMID000000132197 BMID000000132198 BMID000000132199 BMID000000132200 BMID000000132201 BMID000000132202 BMID000000132203 BMID000000132204 BMID000000132205 BMID000000132206 BMID000000132207 BMID000000132208 BMID000000132209 BMID000000132210 BMID000000132211 BMID000000132212 BMID000000132213 BMID000000132214 BMID000000132215 BMID000000132216 BMID000000132217 BMID000000132218 BMID000000132219 BMID000000132220 BMID000000132221 BMID000000132222 BMID000000132223 BMID000000132224 BMID000000132225 BMID000000132226 BMID000000132227 BMID000000132228 BMID000000132229 BMID000000132230 BMID000000132231 BMID000000132232 BMID000000132233 BMID000000132234 BMID000000132235 BMID000000132236 BMID000000132237 BMID000000132238 BMID000000132239 BMID000000132240 BMID000000132241 BMID000000132242 .
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
Project description:In this study we perform a transcriptomics analysis of two maize (Zea mays) organs, roots and leaves, from plants grown in the presence of a sufficient (1000 uM) or limiting (10 uM) concentration of soil phosphate. Overall design: Duplicate root and leaf mRNA profiles for plants grown in the presence of 1000 uM or 10 uM soil phosphate.
Project description:We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 13 parental inbred lines (4 Dent, 9 Flint) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial. Overall design: Four seedlings of each maize inbred line (9 Flint lines: F005, F012, F013, F023, F030, F034, L005, L007, L012; 4 Dent lines: P006, P033, S002, S028) as well as of two control lines (F043, S067) were grown for 7 days under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 per cent air humidity) with randomized plate positions. The whole 7-day-old-seedlings were sampled and frozen in liquid nitrogen. The biological replicates were pooled and homogenized prior to RNA extraction.