In silico mapping on the Chinese Spring deletion map was conducted at Graingenes (http://wheat.pw.usda.gov/GG2/blast.shtml).shtml
Analyses of the bisulfite-sequencing results were conducted at the Kismeth website (http://katahdin.mssm.edu/kismeth).edu/kismeth
Hybridizations were conducted at the DNA Core Facility, University of Missouri (http://biotech.rnet.missouri.edu/dnacore), following the standard Affymetrix procedures (Affymetrix, Santa Clara, CA).
Genotyping was conducted at the Genomix4Life S.r.l (http://www.genomix4life.com) using 250 ng of DNA per accession following the manufacturer's protocol for the Illumina Infinium assay.
Genotyping of tag SNPs from 48 candidate gene regions involved in TNF/NF-κB pathway was conducted at the NCI Core Genotyping Facility Advanced Technology Centerr, Gaithersburg, MD; http://snp500cancer.nci.nih.gov) [45] using a custom-designed GoldenGate assay (Illumina, www.illumina.com).
This was conducted at the NCBI server using BLAST (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi).nih.gov/blast/Blast.cgi
Illumina sequencing was conducted at Beijing Novogene Biological Information Technology Co., Ltd., Beijing, China (http:// www.novogene.cn/) by using Illumina TruSeq™ RNA Sample Preparation Kit (Illumia, San Diego, USA) following manufacturer's recommendations [ 27].
High performance computing was conducted at the New Zealand eScience Infrastructure (NeSi- http://www.nesi.org.nz) with support and guidance from Vladimir Mencl, Markus Binsteiner and Yuriy Halytskyy.
To verify the identity of the sequences generated, a search was conducted at GenBank database sequences using Blast (http://blast.ncbi.nlm.nih.gov/Blast.cgi PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome).nih.gov/Blast.cgi PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Gene expression assays were conducted at the Rutgers University Cell and DNA Repository (RUCDR, http://www.rucdr.org).
