er α chromatin immunoprecipitation (chip) sequencing (seq) or chip-pcr analyses  (Active Motif)

Journal: Nature genetics

Article Title: ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer.

doi: 10.1038/s41588-019-0554-0

Figure Lengend Snippet: Fig. 2 | ARID1A impacts the accessibility of several transcription factor motifs involved in luminal differentiation. a, Volcano plot of ATAC-seq assays in control and ARID1A KO cells. The x axis shows the log2 fold change and the y axis shows the −log10(P). The red dots represent a significant increase in chromatin accessibility (1,701 sites) whereas the green dots represent a significant decrease in chromatin accessibility (3,537 sites) (absolute log2 fold change > 0.5 and Benjamini–Hochberg-adjusted P < 0.05). b, Heatmap of significantly differentially accessible sites in MCF7 cells expressing three distinct sgRNAs against ARID1A and two control sgRNAs (4,608 differential peaks; log2 fold change > 0.5 and Benjamini–Hochberg-adjusted P < 0.05). c, Pie chart showing the distributions of differential peaks to various genic parts. d, Heatmap of H3K27ac ChIP-seq in the differentially accessible sites obtained by ATAC-seq on ARID1A loss (±2-kb regions centered at the peak summit). PSS, peak start site; PES, peak end site. e, Box plot showing the mean signal across peaks that lost chromatin accessibility on ARID1A KO. Also shown is the H3K27ac ChIP-seq differential binding in control and ARID1A KO cells. P values are as shown. A two-sided Mann–Whitney U-test and effect size (Rosenthal’s coefficient) are also shown. The log2 fold change calculated as log2 (mean KO/mean control) is also shown (n = 15). The box shows the 25th, median and 75th percentiles with the whiskers extending to ±1.5× interquartile range (IQR). f, Top significant transcription factor motifs enriched in the lost or gained accessible sites on ARID1A KO as analyzed by a ridge regression model (FDR < 0.01). The x axis represents the ridge regression coefficients.

Article Snippet: Antibodies Antibodies used for ChIP-seq are ER (SC-543, Santa Cruz), H3K27ac (ab4729, Abcam), GRHL1 (Novus Biologicals, NBP1-81321) and FOXA1 (ab23738, Abcam).

Techniques: Control, Expressing, ChIP-sequencing, Binding Assay, MANN-WHITNEY

Journal: Nature genetics

Article Title: ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer.

doi: 10.1038/s41588-019-0554-0

Figure Lengend Snippet: Fig. 4 | ARID1A loss causes defects in SWI/SNF targeting to chromatin at luminal lineage-determining transcription factor loci. a, Heatmap of the ChIP-seq profiles of the SWI/SNF binding sites, as probed by the overlap of BAF155/BRG1 peaks (14,007 common peaks) for the core subunits in control and ARID1A mutant MCF7 cells shown in a horizontal window of ±2 kb from the peak center. The experiment was conducted once. b, Enrichment of BAF155 and BRG1 occupancy in the differentially accessible sites observed by ATAC-seq. The experiment was conducted once. PC, peak center. c, Box plot representing the mean signal across peaks that lose chromatin accessibility on ARID1A KO cells. Also shown are the BAF155 and BRG1 ChIP-seq differential binding in control and ARID1A KO cells. P values were calculated using a two-sided Mann–Whitney U-test; the effect size (Rosenthal’s coefficients) was calculated as described in the Methods. The log2 fold change, which was calculated as log2 (mean KO/mean control) is also shown (n = 13). The box shows the 25th, median and 75th percentiles with the whiskers extending to ±1.5× IQR. d, Motif enrichment of transcription factors found in lost BAF155/ BRG1 sites on ARID1A silencing; n = 9,555 peaks, P values were calculated using CentriMo v.4.11.4. e, ChIP-seq tracks of BRG1 and BAF155 in control and ARID1A KO cells. The experiment was conducted once. f, ChIP-seq profiles for GRHL1 (generated in this study), FOXA1 (ENCODE ENCSR126YEB), GATA3 (ENCODE ENCSR000BST), FOS/JUN (ENCODE ENCSR176EXN) and JUND (ENCODE ENCSR000BSU) at the predicted motif sites obtained from lost SWI/SNF binding sites after ARID1A loss (n = 1).

Article Snippet: Antibodies Antibodies used for ChIP-seq are ER (SC-543, Santa Cruz), H3K27ac (ab4729, Abcam), GRHL1 (Novus Biologicals, NBP1-81321) and FOXA1 (ab23738, Abcam).

Techniques: ChIP-sequencing, Binding Assay, Control, Mutagenesis, MANN-WHITNEY, Generated