Journal: Nature Communications

Article Title: ΔNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer

doi: 10.1038/s41467-022-28202-1

Figure Lengend Snippet: a Schematic of isolation of ΔNp63 fl/fl ; Rosa M/M and ΔNp63 Δ/Δ ; Rosa Δ/Δ basal cells for RNA-seq and ChIP-seq. b Pathway analysis of differentially expressed genes between ΔNp63 fl/fl ; Rosa M/M and ΔNp63 Δ/Δ ; Rosa Δ/Δ basal cells. c ΔNp63 motif derived from basal cell ΔNp63 ChIP-seq compared to published p63 motif. d H3K27ac ChIP-seq signal area under peak for top 500 enhancers in the indicated samples. Data were mean ± SD, n = 3, **** vs. respective ΔNp63 fl/fl ; Rosa M/M , P < 10 −6 , two-tailed Student’s t -test. e Ranking of top 2000 enhancers based on H3K27ac ChIP-seq in ΔNp63 fl/fl ; Rosa M/M (blue) and ΔNp63 Δ/Δ ; Rosa Δ/Δ (red) basal cells. f qRT-PCR of the indicated genes in ΔNp63 fl/fl ; Rosa M/M and ΔNp63 Δ/Δ ; Rosa Δ/Δ basal cells. Data were mean ± SD, n = 3, * vs. ΔNp63 fl/fl ; Rosa M/M , P < 0.05, *** vs. ΔNp63 fl/fl ; Rosa M/M , P < 0.0001, two-tailed Student’s t -test. g , h ChIP-seq profiles of ΔNp63 fl/fl ; Rosa M/M basal cells for the indicated tracks in the Krt5 ( g ) and Bcl9l ( h ) loci. Source data are provided as a Source Data file.

Article Snippet: Low cell number ChIP-seq for H3K27ac (39193, Active Motif), RNA polymerase 2 (39097, Active Motif), and ΔNp63 (sc-8609, Santa Cruz) was performed by Active Motif.

Techniques: Isolation, RNA Sequencing, ChIP-sequencing, Derivative Assay, Two Tailed Test, Quantitative RT-PCR

Journal: Nature Communications

Article Title: ΔNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer

doi: 10.1038/s41467-022-28202-1

Figure Lengend Snippet: a Schematic of isolation of ΔNp63 fl/fl ; Rosa M/M and ΔNp63 Δ/Δ ; Rosa Δ/Δ AT2 cells for RNA-seq and ChIP-seq. b ΔNp63 motif derived from AT2 cell ΔNp63 ChIP-seq compared to published p63 motif. c Ranking of top 2000 enhancers based on H3K27ac ChIP-seq in ΔNp63 fl/fl ; Rosa M/M (blue) and ΔNp63 Δ/Δ ; Rosa Δ/Δ (red) AT2 cells. d qRT-PCR of the indicated genes in ΔNp63 fl/fl ; Rosa M/M and ΔNp63 Δ/Δ ; Rosa Δ/Δ AT2 cells. Data were mean ± SD, n = 3, * vs. ΔNp63 fl/fl , P < 0.05, two-tailed Student’s t -test. e , f ChIP-seq profiles of ΔNp63 fl/fl ; Rosa M/M AT2 cells for the indicated tracks in the Etv5 ( e ) and Bcl9l ( f ) loci. Source data are provided as a Source Data file.

Article Snippet: Low cell number ChIP-seq for H3K27ac (39193, Active Motif), RNA polymerase 2 (39097, Active Motif), and ΔNp63 (sc-8609, Santa Cruz) was performed by Active Motif.

Techniques: Isolation, RNA Sequencing, ChIP-sequencing, Derivative Assay, Quantitative RT-PCR, Two Tailed Test

Journal: Nature Communications

Article Title: ΔNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer

doi: 10.1038/s41467-022-28202-1

Figure Lengend Snippet: a Venn diagram overlaying the genes associated with the top 2000 enhancers in AT2 and basal cells. b Schematic of dCas9-p300 and dCas9-ΔNp63 sgRNA experiment. c – e Relative expression levels of ETV5 ( c ), BCL9L ( d ) and KRT5 ( e ) in 293 T cells over-expressing the indicated constructs. Data were mean ± SD, n = 3, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, two-tailed Student’s t -test. f – h qRT-PCR of ChIP assays for p300, H3K27ac and ΔNp63 at the indicated sites. Data were mean ± SD, n = 3, * vs. shNT, P < 0.05, two-tailed Student’s t -test. Source data are provided as a Source Data file.

Article Snippet: Low cell number ChIP-seq for H3K27ac (39193, Active Motif), RNA polymerase 2 (39097, Active Motif), and ΔNp63 (sc-8609, Santa Cruz) was performed by Active Motif.

Techniques: Expressing, Construct, Two Tailed Test, Quantitative RT-PCR