Demographic and sample parameters of successful culture in scalp (n = 146).

<p>OR = odds ratio, AA = African-American, W = White, PMI = postmortem interval, BMI = body mass index, F = female, M = male, VA = Virginia, DC = District of Columbia; Tox = toxicology testing in blood or vitreous humor; * = p<0.05.</p

Fibroblast characterization: FSP-1 protein expression by immunofluorescence staining and cell proliferation assay in dura and scalp. A.

<p>The morphology of postmortem fibroblast cells generated from (a) dura and (b) scalp. Cultured cells from both sources macroscopically looked similar to what is seen in living skin fibroblast cells, with more enriched cytoplasm and spindle-shaped nuclei under phase-contrast microscopy. Cells from (c) dura and (d) scalp express cytoplasmic Fibroblast Specific Protein-1 (FSP-1) (green). Original scale bars = 35 µm. <b>B.</b> Results from cell proliferation assay in 8 fibroblast cell lines (dura and scalp from 4 individuals) in five different densities. Cell viability was determined in 24 hrs and 48 hrs by WST-8 assay. Values are the mean of results from six wells. Bars ± SE. Scalp fibroblast cell lines grew 1.27-fold faster in the same period than dura fibroblast cells. <b>C.</b> Differences in cell proliferation between scalp and dura by one-way ANOVA; scalp cell growth was significantly more rapid than dura cell growth at 24 hr and 48 hr intervals [F (1, 46) = 12.94, p<0.008].</p

iPSCs generated from one dura fibroblast line express pluripotency markers and differentiate to neuronal fates.

<p>Undifferentiated iPSCs express pluripotency markers NANOG (A) and SOX2 (B). Upon neural differentiation, these cells express neuroectoderm marker SOX1 (C). Temporal gene expression analysis also shows a decrease in pluripotency marker OCT4 (POU5F1) and an increase in <i>PAX6</i> expression by quantitative RT-PCR (D). iPSC-derived neurons express βIII-tubulin and MAP2 (E–G).</p

Odds ratio of culture success: dura vs. scalp matched pairs (n = 53).

<p>No = not successful, Yes = successful.</p

Percentage of successful growth in dura (n = 53) vs. scalp (n = 146) samples.

<p>Sample of 146 scalp and 53 dural specimens. The odds of successful culture in dura were nearly 2-fold compared to scalp.</p

Regional DNA methylation changes manifest in the transcriptome.

<p>(A) Plot of the DNAm levels (proportion methylation) of an example significant DMR, which overlaps the gene SIM1. (B) Plot of the average DMR DNAm levels versus the expression level of <i>SIM1</i>, showing high positive correlation (p = 4.67x10⁻⁸).</p

Increased methylome distances within scalp-derived fibroblasts.

<p>Y-axis: methylome (Euclidean) distance between pairs of samples stratified by cell and tissue types. CD4T: CD4+ T-cell, NK: natural killer cell, Mono: monocyte, NeuN+: neuronal DLPC cell, NeuN-: non-neuronal DLPFC cell.</p

intropolis: exon-exon junctions across publicly available RNA-seq samples on the Sequence Read Archive

All exon-exon junctions detected by Rail-RNA across 21,504 human RNA-seq samples from the Sequence Read Archive, as studied in the paper "Human splicing diversity across the Sequence Read Archive" by Abhinav Nellore, Andrew E. Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A. Phillips III, Nishika Karbhari, Kasper D. Hansen, Ben Langmead, and Jeffrey T. Leek. File formats are described at http://intropolis.rail.bio

Long-range DNA methylation changes manifest in the transcriptome.

<p>(A) Plot of the DNAm levels (proportion methylation) of a significant DNAm block overlapping genes in the <i>HOX</i> family. Y-axis: proportion DNAm levels, x-axis: genomic coordinates on chromosome 17. (B) Corresponding expression levels of the <i>HOX</i> genes within the DNAm block are more highly expressed in the scalp. Y-axis: log₂ transformed fragments per kilobase per million mapped (FPKM), x-axis: sampling location.</p

DNA methylation patterns in dura- and scalp-derived fibroblasts.

<p>(A) Histogram of difference in DNAm levels at CpGs/probes between scalp and dura derived fibroblasts (on the proportion methylation scale). (B) The first principal component (PC1) of the DNAm data plotted against fibroblast sampling location (scalp versus dura). (C) Example significant differentially methylated region (DMR) that overlaps the gene <i>RUNX3</i>, with DNAm levels on the y-axis and genomic coordinates on the x-axis. (D) Example significant DNAm block, with DNAm levels on the y-axis and genomic coordinates on the x-axis. Gene annotation panels in C and D are based on Ensembl annotation–dark blue represents exons and light blue represents introns.</p