Transcription factors with Perturb-seq knockdown data for CCNO-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 = CCNO-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 CCNO-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 |
|---|---|---|---|---|
| chr5:55,029,649–55,030,875 | 203.6 kb | Distal (>10kb) Multiome | 91 | |
| chr5:55,172,818–55,174,056 | 60.6 kb | Distal (>10kb) Multiome | 485 | |
| chr5:55,176,186–55,176,916 | 57.4 kb | Distal (>10kb) Multiome | 520 | |
| chr5:55,220,318–55,221,200 | 13.2 kb | Distal (>10kb) Multiome | 183 | |
| chr5:55,226,323–55,227,998 | 7.3 kb | Proximal (<10kb) Multiome | 708 | |
| chr5:55,232,241–55,234,359 | 215 bp | At TSS Multiome | 615 | |
| chr5:55,307,204–55,308,263 | 73.8 kb | Distal (>10kb) Multiome | 873 | |
| chr5:55,406,222–55,406,887 | 172.6 kb | Distal (>10kb) Multiome | 40 | |
| chr5:55,484,537–55,485,441 | 250.9 kb | Distal (>10kb) Multiome | 208 | |
| chr5:55,497,392–55,498,099 | 263.8 kb | Distal (>10kb) Multiome | 88 |
Genomic view of the CCNO-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.