Transcription factors with Perturb-seq knockdown data for CNN3-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 = CNN3-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 CNN3-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 |
|---|---|---|---|---|
| chr1:94,819,759–94,820,829 | 107.0 kb | Distal (>10kb) Multiome | 576 | |
| chr1:94,854,217–94,855,200 | 72.7 kb | Distal (>10kb) Multiome HiCAR | 530 | |
| chr1:94,925,541–94,928,082 | 54 bp | At TSS Multiome | 926 | |
| chr1:94,929,767–94,930,139 | 2.4 kb | Proximal (<10kb) | 38 | |
| chr1:95,061,557–95,061,908 | at TSS | At TSS | 44 | |
| chr1:95,068,829–95,069,314 | 7.2 kb | Proximal (<10kb) | 177 | |
| chr1:95,069,417–95,069,586 | 7.8 kb | Proximal (<10kb) | 124 | |
| chr1:95,072,438–95,073,470 | 145.5 kb | Distal (>10kb) Multiome | 851 | |
| chr1:95,116,608–95,118,188 | 190.0 kb | Distal (>10kb) Multiome | 748 |
Genomic view of the CNN3-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.