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Briefly, on each map, we performed Principal Component Analysis, and the first component was taken.
To construct the linkage map, we performed re-sequencing of the parents and designed BeadArray markers using detected single nucleotide polymorphisms (SNPs).
Then, for each noisy contact map we performed 10 different reconstructions.
Using phenotypic values, as mentioned above, and our linkage map, we performed a QTL analysis for GA-responsive TIL, LEI and NEI (qGTIL, qGLEI and qGNEI).
To address zinc dependent gene regulation in MAP we performed RNA deep sequencing technique using 50 bp single-ends sequencing on a HiSeq2500 (Illumina, San Diego, CA).
To establish a reference gene-based genetic map, we performed exome sequencing of 14729 genes on a mapping population of 72 haploid samples, generating a resource of 7434 sequence variants segregating for 3787 genes.
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To test the temporal stability (i.e., repeatability) of S-maps, we performed the following three-step analysis.
With eigenvector centrality maps we performed paired t tests between the placebo and exenatide conditions for each scanning block.
After the mutational mapping, we performed in silico mutagenesis to observe the effects of the mutations on the interactions.
In order to interpret the maps, we performed flexible fitting of suilysin domains from the crystal structure.
Difference Mapping We performed 2D difference mapping between class averages by first aligning, rotating, and shifting them in IMAGIC (van Heel et al., 1996 ) using the MSA-ALIGN command.
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