Journal: Genome Medicine

Article Title: Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network

doi: 10.1186/s13073-016-0329-5

Figure Lengend Snippet: eQTLs are independent of total magnitude of gene expression and not preferentially associated with active enhancer marks. a Expression of TNFSF and TNFRSF members was measured by the NanoString nCounter analysis system. Each point represents average expression over eight or more individuals, including healthy controls and individuals with IBD. Genes are listed left to right in order of decreasing number of cell types in which an eQTL was detected. b Average H3K27ac ChIP-seq or input DNA sequencing counts per million intersecting TNFSF-related eQTL SNPs in the same cell type are plotted. c Average H3K27ac ChIP-seq counts per million intersecting eQTL SNPs in the same cell type are compared with a random distribution of intersections created by selecting the same number of SNPs from the cis genomic regions used for eQTL search. Error bars represent the standard deviation of 10,000 iterations of random selection. d eQTL chi-squared scores from the strongest eQTL SNP for each TNFSF-related gene (regardless of whether the association passed our eQTL significance threshold) are compared with H3K27ac ChIP-seq or input DNA sequencing counts per million at the same SNPs. Spearman correlation coefficient ( rho ) and correlation p values ( p ) are indicated for H3K27ac ChIP-seq counts per million versus eQTL score

Article Snippet: H3K27ac ChIP-seq data are available from the NIH Roadmap Epigenomics Project ( http://nihroadmap.nih.gov/epigenomics/ ).

Techniques: Gene Expression, Expressing, ChIP-sequencing, DNA Sequencing, Standard Deviation, Selection

Journal: bioRxiv

Article Title: Lamina-associated polypeptide 2α is required for intranuclear MRTF-A activity

doi: 10.1101/2021.01.08.425886

Figure Lengend Snippet: (A) Venn diagram showing overlap of MRTF-A peaks in WT and Lap2α KO cells under serum-stimulated (15%) conditions from chromatin immunoprecipitation followed by deep-sequencing (ChIP-seq). (B) MEME-ChIP analysis identifies SRF motif (upper part) within the MRTF-A peaks found in 15% FBS (upper table) and peaks present in 15% FBS but absent in 0.3% FBS (lower table). (C) Binding of Pol II S5P and MRTF-A on MRTF-A target genes Acta2 and Vcl in Lap2α WT and KO MDFs in serum-starved (0,3%) and stimulated (15%) conditions. (D) Coverage of MRTF-A on the peaks with SRF motif in Lap2α WT vs KO cells in serum-starved (0,3%) and serum-stimulated (15%) conditions.

Article Snippet: ChIP libraries were prepared for Illumina NextSeq 500 using NEBNext ChIP-Seq DNA Sample Prep Master Mix Set for Illumina (NEB E6240) and NEBNext ® Multiplex Oligos for Illumina ® (Index Primers Set 1) (NEB E7335) according to the manufacturer’s protocols.

Techniques: Chromatin Immunoprecipitation, Sequencing, ChIP-sequencing, Binding Assay

Journal: bioRxiv

Article Title: Lamina-associated polypeptide 2α is required for intranuclear MRTF-A activity

doi: 10.1101/2021.01.08.425886

Figure Lengend Snippet: (A) Binding of Pol II S5P, MRTF-A, H3K9Ac, H3K4me3 and Lap2α by ChIP-seq to MRTF-A target gene Vcl in Lap2α WT and KO fibroblasts under serum starved (0,3%) and serum stimulated (15%) conditions. Data for H3K9Ac and H3K4me3 binding were used from (B) Coverage of Lap2α and MRTF-A on MRTF-A peaks with SRF motif in Lap2α WT and KO MDFs cells in serum-starved (0.3%) and serum-stimulated (15%) conditions. (C) Histone modifications at the TSS of 36 selected genes (genes that contained MRTF-A peaks with an SRF-binding motif on their promoters, Table S3.2 ) in WT and KO MDF. Left: H3K4me3; right: H3K9Ac (D) Histone modifications at the TSS of all expressed genes in WT and KO MDF. Left: H3K4me3; right: H3K9Ac

Article Snippet: ChIP libraries were prepared for Illumina NextSeq 500 using NEBNext ChIP-Seq DNA Sample Prep Master Mix Set for Illumina (NEB E6240) and NEBNext ® Multiplex Oligos for Illumina ® (Index Primers Set 1) (NEB E7335) according to the manufacturer’s protocols.

Techniques: Binding Assay, ChIP-sequencing

Journal: bioRxiv

Article Title: Intrinsic epigenetic state of primary osteosarcoma drives metastasis

doi: 10.1101/2023.11.09.566446

Figure Lengend Snippet: (A) Schematic showing the generation of patient-derived xenografts (PDX) from primary OS tissues for each of the following categories; primary tumor obtained from the localized site that did not metastasize – localized; primary tumor obtained from the localized site that eventually underwent metastasis - primary met ; tumor obtained from primary site after surgery and chemotherapy – local control ; metastatic tumor obtained from a distal site – distal met . The PDX’s subsequently underwent transcriptomic by RNA-seq and epigenomic profiling by ATAC-seq and ChIP-seq for H3K27ac. (B) Shows the overlap between the H3K27ac peaks detected for each sample using intervene tools. (C) Principal component analysis of signal intensity (tags per million) of top 20% most variable regions by median absolute deviation (n = 31,690) of all H3K27ac enriched peaks. (D) Shows the fraction of H3K27ac enriched peaks (n = 158,455) overlapping with different genomic annotations. Peaks overlapping within ±LJ2.5KB of any annotated transcription start site were considered to be promoter associated peaks (22.90%); peaks overlapping with 5’UTR, coding exons, introns, and 3’UTRs were considered to be in gene bodies (40.50%) and all the remaining peaks were considered to be intergenic peaks (36.60%). (E) Left - Heatmaps of average H3K27ac activity ±LJ3LJKb relative to the center of the detected peak for localized (yellow), primary met (green), local control (red) and distal met tumors (purple), metaplots showing the average levels of H3K27ac on top each of the heatmap (top). These regions were identified to be enriched for H3K27ac signal in every sample (n = 6,086). Right - Heatmaps of average chromatin accessibility at the corresponding locus for every row in D, metaplots showing the average chromatin accessibility on top each of the heatmap (top)

Article Snippet: The ChIP-seq experiment has been conducted by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode Cat# G02010000).

Techniques: Derivative Assay, RNA Sequencing Assay, ChIP-sequencing, Activity Assay