Additional file 6: Table S2. of Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Median absolute difference between technical replicate pairs. (DOCX 14 kb

Additional file 4: Figure S3. of Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Density distribution of β values for imprinted differentially methylated regions. Density plots for raw (A), stratified QN (C) and stratified QN with ComBat (E) for 227 probes mapping known imprinted differentially methylated regions. Each line represents a sample, with samples coloured by batch. As methylation at these loci is allele-specific there is a single density distribution rather than the bimodal distribution seen in Additional file 3: Figure S2. The standard error-type measure (DMRSE) diminishes with Stratified QN and ComBat, indicating more reliable data. B, D and F show the Infinium I and II probe distributions, which becomes more uniform with stratified QN and ComBat. (PDF 4133 kb

Additional file 7: Table S3. of Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Standard error measures for imprinted differentially methylated regions for the various normalisation methods. (DOCX 13 kb

Additional file 1: Table S1. of Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Clinical data and sample extraction and storage information. (DOCX 20 kb

DataSheet1.docx

<p>Blue whales are little studied, face significant anthropogenic threats and within the Northern Indian Ocean, have a restricted range, making them an archetype for conservation needs of megafauna around the world. We studied feeding behavior of blue whales using dietary DNA metabarcoding of fecal samples. While globally blue whale populations feed predominantly on Euphausiidae, 87% of prey DNA amplicons extracted from fecal samples from this population were sergestid shrimp, demonstrating that blue whales can locate and feed on dense swarms of other types of prey when they occur. Within the Indian Ocean sergestids are present within the top 300 m, which correlates with the deep scattering layer observed by hydroacoustics. Studies suggest that this requirement to dive deeper in search of prey likely explains the prevalence of fluke up diving within this population of blue whales relative to other parts of the globe. Furthermore, this study revealed the presence of acanthocephalan endoparasites within the stomach and intestines of the Northern Indian Ocean blue whales. This represents the first record of Acanthocephala in blue whales in the Northern Indian Ocean and highlights the need for further studies on both the ecto- and endoparasitic flora and monitoring of health of these cetaceans for their management and conservation.</p

Additional file 3: Figure S2. of Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Density distribution of β values and multidimensional scaling plots of M values for replicate samples. Density (A, C, E) and MDS (B, D, F) plots of three replicate sample groups for raw (A, B), stratified QN (C, D) and stratified QN ComBat-corrected (E, F) data. For all plots, samples are coloured by batch 1–3 as labelled. Density plots show the distribution of β values, which become more uniform after stratified QN (C) and stratified QN plus ComBat (E). MDS plots show clustering of the 1000 most variable sites by M value, highlighting the decreasing variance between replicate groups after stratified QN and ComBat (F). (PDF 7387 kb

Additional file 2: Figure S1. of Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Hierarchical cluster dendrogram for raw, stratified QN and ComBat-corrected data. Samples are clustered by similarity and labelled by batch. Raw data samples (A) clearly cluster into three distinct batches while stratified QN (B) partially adjusts clustering by batch and stratified QN combined with ComBat considerably diminishes the batch effect (C). Red stars indicate replicate samples which cluster more clearly in (C), indicating removal of batch effects. (PDF 449 kb

Detectable levels of PrP^Sc on Western blots do not correlate with the levels of infectivity.

<p>10% brain homogenates from an uninfected brain (lane 2) time-course samples week 3, 6, 9, 12, 15, 18, 21 (lane 3–9), and the terminal sample (lane 10) were digested with proteinase K at 60°C for 10 minutes and assessed by Western blot. The observed signal does not correspond with the levels of infectivity found in corresponding bioassays for the week 12–21 post-exposure time-points.</p

Comparison of the cull dates for the mice challenged via the gingival margin.

<p>Panel A; Frequency distribution plots show the presence of a normally distributed population with a mean incubation period of around 250 days plus a small number of animals with significantly shorter incubations ranging from 140–188 days. Panel B; when these two groups are compared they show distinct means and distribution and are considered as distinct populations (p<0.001).</p