Thushangi N. Pathiraja

The Impact of Gamification on Student Engagement and Learning in Science: A Study on Team Jeopardy

Thushangi N. Pathiraja, Akshan S. Ranasinghe

Student engagement in a science classroom is challenging and most students perceive science courses as difficult. Gamification is an emerging strategy used by educators across various disciplines to increase student engagement and promote active learning. One known gamification technique is team Jeopardy, …

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Integrative genomic analyses of European intrahepatic cholangiocarcinoma: Novel ROS1 fusion gene and PBX1 as prognostic marker

Patrick Sven Plum, Timo Hess, Denis Bertrand, Isabelle Morgenstern et autres

BACKGROUND: Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct with a poor prognosis owing to limited therapeutic options. The incidence of intrahepatic CCA (iCCA) is increasing worldwide, and its molecular basis is emerging. Environmental factors may contribute to regional differences …

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Supplementary Figure 3 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Figure S3. Mapping efficiency was above 50 for all samples in both time points. One sample was an outlier in the early time point (P12) and one at the late time point (NP4) and were removed from further analysis. Both Pearson …

Supplementary Table 1 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Primers used for quantitative PCR and bisulfite sequencing.

Supplementary Data 1 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Data 1. This spreadsheet contains the results of the differential methylation analysis, the meta-analysis and the pathway analysis. In the meta-analysis sheets, the first 3 columns represent the chromosomal locations, followed by the significance level (stat, p-value, and FDR). Weight.1 and …

Supplementary Figure Legends from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

All Supplementary Figure legends are included in this document.

Supplementary Figure 5 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Fig S5. Imprinted genes display approximately 50% DNA methylation. Gene regions known to be imprinted were chosen to confirm the validity of the Methyl-Seq assay. For each gene a β value was calculated for each window. The frequency of each particular …

Supplementary Figure 4 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Figure S4. Full representation of CpG methylation analysis in the confirmation of Methyl-Seq DNA methylation by bisulfite sequencing. (A) The percent methylation for each CpG site after bisulfite sequencing on mammary gland genomic DNA is represented. Each of the top differentially …

Supplementary Figure 6 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Figure S6. Supervised hierarchical clustering and cell type content analysis. (A) Heatmaps displaying supervised hierarchical clustering of hypermethylated and hypomethylated windows including dendrograms (Red=Methylated, Green=Unmethylated).

Supplementary Figure 9 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Fig S9. Differentially methylated regions of IGF pathway genes align with histone methylation sites. The UCSC Genome Browser was used to align the Irs1, Igf1, and Igfbp4 with other epigenetic modifications. The red bars indicate the regions of differential DNA methylation …

Supplementary Figure 7 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplemental Fig S7. Igf1r is central to a top signaling network in Ingenuity pathway analysis. Ingenuity pathway analysis (IPA) identified this signaling network to be significantly altered by DNA methylation. The hyper and hypomethylated genes identified to be persistently differentially methylated by …

Supplementary Figure 1 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth et autres

Supplementary Figure S1. Experimental design and quality control analysis for Methyl-Seq data. (A) FVB mice were bred to become pregnant (parous, P) and underwent a complete pregnancy (Pr), lactation (L), and Involution (I). Animals were then euthanized immediately after involution (Early, E), …