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Supplementary Figures – Sex- and tissue- specific effects of binge levels of prenatal alcohol consumption on DNA methylation at birth

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posted on 2021-11-29, 11:31 authored by Taylor & FrancisTaylor & Francis, Loke Y.J, Muggli E, Saffery R, Ryan J, Lewis S, Elliott E.J, Halliday, J, Craig J.M

Supplementary Figure 1. Number of probes removed in each data filtering step

The chart illustrates the number of probes removed due to bad probe signal (detection p > 0.01), annotation of SNPs, non-specific target, and annotation on sex chromosomes.

Supplementary Figure 2. Principal component analysis (PCA) plots of buccal and placenta datasets before and after batch adjustment using the ComBat algorithm.

(A)-(D) PCA plots are coloured and labelled based on sample chip number in buccal and placenta datasets. (E) Table lists P values of univariate regression between top three PCs and sample chip number.

Supplementary Figure 3. Cell type proportions estimated in buccal and placenta samples.

(A)–(B) Boxplots illustrates proportions of epithelial, fibroblast and immune cell types in buccal and placenta. The thick lines in in the boxes represent the median, the boxes represent data within the 25th and 75th percentile range, whiskers represent 5th to 95th percentile range. The circles are the outliers.

(C)-(D) Correlation plots between each cell type proportion. Epi = Epithelial; Fib =Fibroblast; IC = Immune cells.

Supplementary Figure 4. Scree plots of the first ten PCs in both tissues and sexes.

For buccal samples, PCs 1-5 and PCs 1-6 capture most data variation in male and female dataset, respectively. For placenta samples, PCs 1-6 and PCs 1-8 capture most data variation in male and female dataset, respectively.

Supplementary Figure 5. MDS plots of placenta dataset in (a) male and (b) female offspring.

These MDS plots illustrate that dataset of non-European origin samples (blue circles) are not distinct from European origin samples (red circles) in placenta.


the Australian National Health and Medical Research Council Grant #1011070; Senior Research Fellowship #1021252 (JH) and #1045161 (RS), and Practitioner Fellowship #1021480 (EE)

the Medical Research Futures Fund Next Generation Fellowship #1135959 (EE)

the Victorian State Government’s Operational Infrastructure Support Program

the McCusker Charitable Trust

Jack Brockhoff Foundation #3525

Foundation for Children #2015-111