dtag 7  (MedChemExpress)

Journal: Nature Communications

Article Title: Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions

doi: 10.1038/s41467-024-55403-7

Figure Lengend Snippet: a Frequency of Footprint-C 1D peak sites with 1, 2, 3, or 4+ footprints in K562 or HEK293T. b V-plots are shown for two 1 V sites with tracks from Footprint-C fragment ends, 1D signal, DNase-seq, CTCF and MAZ ChIP-seq. c V-plot is shown for one 3 V site with tracks from Footprint-C fragment ends, 1D signal, DNase-seq, TBP, CTCF and ZNF384 ChIP-seq. d Frequency of each TF with footprints in 1 V or 2 V+ sites in K562 or HEK293T. e Frequency of top 40 TF-TF pairs, from all 2 V sites in K562 or HEK293T. f , h Frequency of motif orientation of all CTCF:CTCF ( f ) or CTCF:FOX ( h ) pairs from 2 V sites in K562 or HEK293T. g , i Screenshots showing tracks from Footprint-C 1D, CTCF, RAD21, FOXK2 ChIP-seq and MNase-seq in K562. j V-plots of three types of CTCF 1 V sites are shown with CTCF and other TF ChIP-seq, and Footprint-C 1D average signal in K562. A diagram is shown at the bottom. The red arrows in b , c , g , i mark the indexed CTCF or FOX motifs.

Article Snippet: The RAD21 degron cells were treated with 1 μM dTAG-7 (MCE, HY-123941) or DMSO as control for 4 h.

Techniques: ChIP-sequencing

Journal: Nature Communications

Article Title: Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions

doi: 10.1038/s41467-024-55403-7

Figure Lengend Snippet: a Frequency of read mate orientation of different Hi-C datasets when distance <1 kb. b A screenshot showing Footprint-C contact heatmap with tracks from H3K27ac, ZNF143, KLF16, CTCF, RAD21 ChIP-seq, total RNA-seq, DNase-seq and Footprint-C 1D in K562. Gray shades mark the positions of non-CTCF loop anchors. c Number of loops (>20 kb) or stripes detected in Footprint-C, Micro-C, or in situ Hi-C datasets at different sampling size or by different methods. d Overlap of Mustache loops between Footprint-C & Micro-C datasets in K562. e Aggregate plots for common or Footprint-C specific loops. f Fraction of different loop types from common or Footprint-C specific loops. Enh, enhancer. Pro, promoter. g Size of common or Footprint-C specific structural A-A or B-B loops. Min: lower end of violin. Q1: lower bound of box. Q2: line in box. Q3: higher bound of box. Max: higher end of violin. P was calculated by two-sided Wilcoxon–Mann–Whitney test. Effect sizes are shown. h Footprint-C (right up) and Micro-C (left down) contact heatmaps at the same sampling size of 1800 M contacts showing one specific A-A (left) or B-B (right) structural loop, with tracks from genome annotation, PC1 value, CTCF, RAD21 or H3K9me3 ChIP-seq. Black squares mark the two loops. i , Aggregate plots of loops in DMSO or dTAG-7 treated HEK293T. The loops were from Footprint-C in WT HEK293T, and were aggregated at the center of a ±200 kb window at 5-kb resolution. The average enrichment score for loops was shown in top left corner. Source data are provided as a Source Data file.

Article Snippet: The RAD21 degron cells were treated with 1 μM dTAG-7 (MCE, HY-123941) or DMSO as control for 4 h.

Techniques: Hi-C, ChIP-sequencing, RNA Sequencing Assay, In Situ, Sampling, MANN-WHITNEY