Transcription factors with Perturb-seq knockdown data for VIRMA-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 = VIRMA-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 VIRMA-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 |
|---|---|---|---|---|
| chr8:94,261,952–94,262,867 | 291.4 kb | Distal (>10kb) Multiome | 569 | |
| chr8:94,436,616–94,437,535 | 116.7 kb | Distal (>10kb) Multiome | 334 | |
| chr8:94,474,579–94,475,673 | 78.7 kb | Distal (>10kb) Multiome | 722 | |
| chr8:94,549,688–94,550,096 | 3.6 kb | Proximal (<10kb) | 32 | |
| chr8:94,553,030–94,554,248 | 123 bp | At TSS Multiome | 938 | |
| chr8:94,562,151–94,562,388 | 8.4 kb | Proximal (<10kb) | 17 | |
| chr8:94,605,142–94,605,744 | 51.8 kb | Distal (>10kb) Multiome | 82 | |
| chr8:94,638,867–94,642,864 | 85.6 kb | Distal (>10kb) Multiome | 705 | |
| chr8:94,719,362–94,720,432 | 166.1 kb | Distal (>10kb) Multiome | 1182 | |
| chr8:94,822,329–94,823,941 | 269.5 kb | Distal (>10kb) Multiome | 818 |
Genomic view of the VIRMA-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.