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Only clear and highly reproducible bands between two technical replications (starting fro the digestion/ligation step) were scored.
Only clear and reproducible variant bands between two technical replications were considered as putative new insertions by the Dart-related TEs, and recovered for sequencing.
Using 16 pairs of selective EcoRI + HpaII/ MspI primer combinations (Additional file 1), 940,922,1,018,1,031,1,017 and 1,013 clear and reproducible MSAP bands (between two technical replications, seeMethods) were scored for the three kinds of samples (seed-plants, calli and regenerants) of each of the six genotypes, as for AFLP.
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For each biological replicates two technical replications were performed (n = 6).
Two reverse transcription reactions (two technical replications) were prepared from each biological replicate.
The cDNA synthesized from six biological replicates was used to perform in RT-qPCR with two technical replications for each sample of each primer pair.
Each data point represents the mean of three NILs (NILs 14-4, 6-4, Y4 for +Pup1; NILs 26-6, 28-10, and Nipponbare for −Pup1), with three biological and two technical replications per NIL.
Each replication was performed based on an independent RNA sample preparation and consisted of two technical replications.
We employed a dye-swap experimental design that included two biological and two technical replications (Figure 1; [42], [42]).
For each biological replication, two technical replications were performed.
At least two technical replications were conducted in each case.
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