Additional file 2: Table S2. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

Expressed protein-coding genes in PANTHER pathways. Expressed protein-coding genes denoted by Ensembl Gene ID (column A), gene name and symbol (column B), Panther family/subfamily (column C), Panther protein class (column D), and average expression in CPM (column E) were assigned to PANTHER defined pathways, which are referred to by name and accession number. Only genes expressed at levels > 1 CPM were considered for analysis. CPM counts per million. (XLSX 172 kb

Additional file 4: Table S4. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

Co-expressed lncRNAs and protein-coding genes in cis. Co-expression of lncRNAs (columns A and B) with their nearest (adjacent or overlapping) protein-coding gene (column D) was determined by the Pearson’s correlation coefficient r (column F). An r value > 0.602 or < −0.602 was regarded as significant (p < 0.05, two-tailed t test, n = 11). Co-expressed lncRNA/protein-coding gene pairs are ranked by the absolute r value. A positive r value indicates positive correlation and a negative r value indicates negative correlation (column G). The distance between lncRNA and protein-coding gene (column H) was defined as the distance between their nearest borders irrespective of strand orientation (columns C, E) and was set 0 for overlapping lncRNAs and protein-coding genes. LncRNAs were positioned upstream, overlapping, and/or downstream of the coding gene body (column I). A number of lncRNAs overlapped the coding gene promoter (column J) defined as the 10 kb upstream sequence of a gene. Only lncRNA and coding genes with average expression levels > 1 CPM (columns K and L) were considered for analyses. LncRNA expression was in most cases less than that of the coding gene (column M). Coding genes function in various biological processes (column N). (XLSX 63 kb

Additional file 1: Table S1. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

Gene list. Read-pairs were aligned by STAR to the mouse reference genome. STAR alignments were run through HTSeq for determination of read-pair counts by genes. Genes are denoted by their Ensembl gene ID, gene symbol, and gene type (columns A–C). EdgeR calculated average gene expression values across all offspring (column D) and fold-changes between nicotine-exposed and control offspring (FC (N/C), column E). EdgeR (column F), baySeq (column G), and DESeq (column H) determined differential gene expression. FDR false discovery rate-adjusted p value, CPM counts per million. (XLSX 2364 kb

Additional file 3: Table S3. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

Expression ranking of lncRNAs in POMC neurons. LncRNA genes referred to by Ensembl Gene ID (column A), gene name (column B), and gene type (column C) were ranked by average expression across all samples (column D). Only lncRNA genes expressed at levels > 1 CPM were considered for analysis. CPM counts per million. (XLSX 98 kb

Additional file 3: of Serum long noncoding RNA HOTAIR as a novel diagnostic and prognostic biomarker in glioblastoma multiforme

Figure S2. A longitudinal study on a single GBM patient was carried out in order to monitor the changes in serum HOTAIR expression over time. 3 different time points were included in this study: pre-op (the blood was drawn right before the surgery started), post-op (at least 24 h after surgery) and during the 2 week follow-up (F/U) with the neurosurgeon. We show that the level of HOTAIR decreases after surgery and at the follow-up visit. (PDF 430 kb

Additional file 1 of Safety and pharmacokinetics of a highly bioavailable resveratrol preparation (JOTROL TM)

Additional file 1

Additional file 1: of Serum long noncoding RNA HOTAIR as a novel diagnostic and prognostic biomarker in glioblastoma multiforme

Supplementary materials and methods. (DOCX 109 kb

Additional file 2: of Serum long noncoding RNA HOTAIR as a novel diagnostic and prognostic biomarker in glioblastoma multiforme

Figure S1. HOTAIR expression detected in our biomarker assay is derived mostly from circulating RNA, not DNA. 3 GBM serum samples were selected at random and the relative HOTAIR expression in GBM serum with and without reverse transcription (RT)-PCR was determined. The HOTAIR RNA was reverse-transcribed into HOTAIR cDNA and qPCR was performed. The circulating HOTAIR DNA in the serum was detected by qPCR without RT. The considerable difference between HOTAIR expression with and without RT demonstrates that the HOTAIR we are detecting in our qRT-PCR reactions is derived from RNA and not DNA. (PDF 1003 kb

Individual screening results.

Bar graphs of clinically actionable drug responses for (A) EAC42 and (B) EAC47.</p

Ex vivo drug sensitivity testing.

(A) The heatmap of sDSSmod profiles reveals large variability in both direction and magnitude of drug responses in the esophageal adenocarcinoma cell lines tested. The sDSSmod profile for each cell line is depicted with all drugs that had a score of more than +5 or less than -5 in at least one cell line (drugs that had no effect in any cell linewere excluded). Cell lines and drugs were clustered using hierarchical clustering with a tanimoto distance metric. Red color indicates a positive sDSSmod score while green color indicates a negative sDSSmod score. Bar graphs of clinically actionable drug responses for (B) OE19 and (C) OE33.</p