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Foreign materials such as stones and insect infested maize were removed through winnowing.
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Maize seedlings were removed from the pots; their roots were immersed in glass tubes filled with 50 mL of 0.01 mol L−1 KOH for 5 min to remove organic anions adhering to the root surfaces.
The maize plants were removed from the pots (by carefully cutting the shoots, avoiding disturbance of the EM) every 3 months and new pre-germinated seeds were planted in order to maintain the continuous growth of plants in the system.
Transcripts with best matches to viral or maize sequences were removed from further analyses.
Indeed, if the maize gluten samples were removed from the dataset then the variance caused by the DNA isolation became lower (data not shown).
WCR adults were no longer present in the field when these maize and Miscanthus plants were removed.
Repeat libraries from other plant species were obtained from the TIGR plant repeat databases and the TIGR maize repeat database, and ribosomal DNA sequences were removed from these databases.
Markers with more than 15% missing data among the 63 phenotyped IBM RIL were removed, leaving 3205 markers across the 10 maize chromosomes.
After mapping to the Swiss-Prot and nr databases (E-value <10-6), 576 contigs were removed from the dataset because they were of maize, bacterial or virus origin.
Two mexicana individuals were removed from subsequent analysis after being identified as recent hybrids with maize in an initial principal component analysis (PCA) that included data from 279 maize inbred lines (Cook et al. 2012).
First, rRNA, tRNA, snRNA, and snoRNA, as well as those containing the polyA tail, were removed from the small RNA sequences and the remaining sequences were compared against maize ncRNAs deposited in the NCBI Genbank database and Rfam database.
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