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After size selection, we amplified the selected fragments using Illumina-supplied PCR primers.
The selected fragments followed the selection strategies for RNAi in wheat [ 53].
Much deeper sequencing will be needed to ensure complete or sufficient coverage of the selected fragments, in comparison to unbiased selection techniques such as PCR.
In methyl-Seq, following digestion with MspI and HpaII, genomic DNA fragments are subjected to size selection to enrich for CpG-containing regions and the selected fragments are sequenced on a next-generation sequencing platform.
The kinetic energies of selected fragments were calculated from the spectra.
Furthermore, boundaries of the selected fragments correlated with domain boundaries as defined by bioinformatics predictions (R2=0.82 p=0.0166).
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We randomly sheared the DNA in each library using an ultrasonicator and then size-selected fragments between 300 to 500 bp.
We size-selected fragments at 400 600 bp by agarose gel electrophoresis, and enriched for fragments with primers on either end by an 18-cycle PCR reaction.
Among these sequences, only one was shared with the DAF-16 DBD-selected fragments, indicating that selection using the DBD generated specific genomic fragments associated with DAF-16 binding elements.
Based on test results from the Zenobia compounds, we subsequently developed and applied a streamlined fragment screening strategy to screen a much larger library consisting of 3000 computationally pre-selected fragments.
Size-selected fragments were end-repaired and ligated to Illumina Paired-End sequencing adapters.
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