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In addition, we used a conservative burn-in value of 1,000 (manual verification of a few replicates indicates that the burn-in is less than 500).
The similarity between different biological replicates indicates that using local information improves methylation-calling accuracy.
Correlation coefficients calculated for each of the replicates indicates that all but two were above 0.9, testifying to the quality of the expression data (See Additional file 2).
An analysis of the SUMO enriched proteome over the three replicates indicates that in total 1821 unique proteins were identified using a cutoff of 95% probability for identification of peptides.
Nevertheless, an interpretation using the strict criteria that no ChIP was observed for the B73 samples, no ChIP was observed for either of the 9Bic-1 replicates, but that ChIP-seq reads covering the entire marker sequence were observed for all three TB-9Sb replicates indicates that at least seven markers lie within the functional B centromere core.
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After labeling both treated and untreated samples with biotin and hybridizing to different sectors of the same 4×2K array, very little difference could be seen between treated and untreated samples (r2 = 0.9 and 0.96 respectively for two replicates) indicating that little DNA contaminates samples (data not shown).
These replicates indicate that representative genetic diversity from the entire spatially structured southern refugium was present along the expansion leading edge, primarily due to the fact that individuals well-inside the southern refugium were participants in the range expansion process.
LoessOnly methods, (established technique for dual-channel arrays), exhibit low fluctuation even in single-channel technical replicates, indicating that, although not developed for this type of data originally, they perform well with respect to the variability criterion.
Pairwise correlation of J2-IP RNA-seq replicates indicated that the J2-IP replicates were highly similar (Supplementary Fig S8).
Experimental and biological replicates indicate that all but one gene in this study escape X inactivation at a reproducible frequency.
The negligible technical variation within replicates indicated that biases related to each method are also reproducible and are not influenced by the setting up of technical replicates.
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CEO of Professional Science Editing for Scientists @ prosciediting.com