Journal: The journal of pain : official journal of the American Pain Society

Article Title: Enrichment of genomic pathways based on differential DNA methylation associated with chronic postsurgical pain and anxiety in children – a prospective, pilot study

doi: 10.1016/j.jpain.2018.12.008

Figure Lengend Snippet: Overlap between CpG sites associated with chronic postsurgical pain (CPSP) and childhood anxiety sensitivity index (CASI) with functional genomics datasets in cells derived from brain tissue

Article Snippet: Roadmap Epigenomics (Histone narrow) , H1 Derived Neuronal Progenitor Cells , H3K4me2 , 0.283 , 0.0002.

Techniques: Functional Assay, Derivative Assay

Journal: Cell stem cell

Article Title: Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells

doi: 10.1016/j.stem.2017.03.009

Figure Lengend Snippet: eQTL Functional Annotation Enrichments. -log10 Fisher exact enrichment p-values for 4,616 eQTL lead SNVs/indels in (A) Roadmap Epigenomics DNase hypersensitivity sites (DHSs) and (B) ENCODE DHSs. The replicate H1 hESC DHS experiments in (B) were performed in different laboratories which may account for their different levels of enrichment. (C) Fisher exact odds ratios for ENCODE H1 hESC transcription factor CHiP-seq peaks. Color indicates whether the enrichment was significant which can vary due to the number of ChIP-seq peaks for each particular mark. See also Table S3.

Article Snippet: We obtained DHSs for the H1, H9, iPS DF 6.9, and iPS DF 19.11 cell lines from Roadmap Epigenomics and merged them into one bed file.

Techniques: Functional Assay, ChIP-sequencing

Journal: Cell stem cell

Article Title: Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells

doi: 10.1016/j.stem.2017.03.009

Figure Lengend Snippet: peQTN Characteristics. (A) Number of stem cell DHSs overlapped by eQTNs for four stem cell lines from Roadmap Epigenomics (H1, H9, iPS DF 6.9, iPS DF 19.11). (B) Number of peQTNs per eGene for 1,526 eGenes with at least one peQTN. (C) Putative eQTN for MED30 that overlaps a CEBPB ChIP-seq peak and disrupts a known CEBPB motif. Scatter plot shows -log10 association p-value from EMMAX for peQTN (purple point), other significant eQTL variants (green points) and variants not associated with MED30 expression (blue points). ENCODE H1 hESC CEBPB ChIP-seq peaks (blue rectangles) and chromHMM chromatin state predictions (multi-color track) are displayed. (D) CTCF ChIP-seq peak coverage (z-score of log10 counts) from five iPSC lines for peaks containing peQTNs predicted to disrupt CTCF binding and that had evidence of CTCF allelic bias in the ChIP-seq data. Counts are stratified by the genotype of the peQTN: 0, 1, and 2 for low, intermediate, and high predicted binding of CTCF, respectively. The peak coverage is significantly associated with the peQTN genotype (r=0.087, p=0.039). (E) The P1 region with the reference allele drives expression in 96% of embryos while the alternate allele leads to a complete loss of expression. (F and G) Image showing tailbud stage Ciona embryo electroporated with (F) Snail P1 (ref. allele) > GFP or (G) Snail P1 (alt. allele) > GFP. Expression can be seen in the tail muscle for the reference allele. Images were taken at the same exposure time to allow for direct comparison. See also Figure S2 and Tables S4 and S5.

Article Snippet: We obtained DHSs for the H1, H9, iPS DF 6.9, and iPS DF 19.11 cell lines from Roadmap Epigenomics and merged them into one bed file.

Techniques: ChIP-sequencing, Expressing, Binding Assay, Comparison