Transcription factors with Perturb-seq knockdown data for NIPBL-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 = NIPBL-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 NIPBL-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 |
|---|---|---|---|---|
| chr5:36,596,123–36,596,706 | 280.2 kb | Distal (>10kb) Multiome | 93 | |
| chr5:36,606,440–36,607,386 | 270.1 kb | Distal (>10kb) Multiome | 471 | |
| chr5:36,618,961–36,619,487 | 257.5 kb | Distal (>10kb) Multiome | 147 | |
| chr5:36,689,905–36,690,922 | 186.2 kb | Distal (>10kb) Multiome | 674 | |
| chr5:36,692,732–36,693,630 | 183.4 kb | Distal (>10kb) Multiome | 332 | |
| chr5:36,701,409–36,702,282 | 174.9 kb | Distal (>10kb) Multiome | 152 | |
| chr5:36,744,113–36,746,060 | 131.9 kb | Distal (>10kb) Multiome HiCAR | 801 | |
| chr5:36,870,542–36,870,736 | 6.0 kb | Proximal (<10kb) | 228 | |
| chr5:36,875,320–36,875,597 | 1.1 kb | Proximal (<10kb) | 305 | |
| chr5:36,875,838–36,877,715 | 111 bp | At TSS Multiome | 929 | |
| chr5:36,878,770–36,879,061 | 2.1 kb | Proximal (<10kb) | 201 | |
| chr5:37,086,434–37,087,024 | 209.9 kb | Distal (>10kb) Multiome | 249 | |
| chr5:37,090,010–37,091,198 | 213.8 kb | Distal (>10kb) Multiome | 257 |
Genomic view of the NIPBL-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.