Transcription factors with Perturb-seq knockdown data for NCK1-DT. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = NCK1-DT upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NCK1-DT, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr3:136,751,181–136,753,220 | 109.5 kb | Distal (>10kb) Multiome | 1046 | |
| chr3:136,818,569–136,819,674 | 43.0 kb | Distal (>10kb) Multiome | 656 | |
| chr3:136,819,787–136,820,421 | 41.8 kb | Distal (>10kb) Multiome | 524 | |
| chr3:136,860,443–136,860,889 | 1.1 kb | Proximal (<10kb) | 111 | |
| chr3:136,861,045–136,862,941 | 146 bp | At TSS Multiome | 966 | |
| chr3:137,032,463–137,033,394 | 170.7 kb | Distal (>10kb) Multiome | 351 |
Genomic view of the NCK1-DT locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.