Transcription factors with Perturb-seq knockdown data for TSKU-AS1. 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 = TSKU-AS1 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 TSKU-AS1, 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 |
|---|---|---|---|---|
| chr11:76,554,474–76,555,062 | 228.3 kb | Distal (>10kb) Multiome | 45 | |
| chr11:76,624,568–76,625,315 | 158.1 kb | Distal (>10kb) Multiome | 105 | |
| chr11:76,670,486–76,671,227 | 112.2 kb | Distal (>10kb) Multiome | 303 | |
| chr11:76,733,962–76,736,172 | 48.9 kb | Distal (>10kb) Multiome HiCAR | 353 | |
| chr11:76,758,769–76,759,574 | 23.8 kb | Distal (>10kb) Multiome | 99 | |
| chr11:76,770,356–76,771,447 | 12.2 kb | Distal (>10kb) Multiome | 371 | |
| chr11:76,781,571–76,782,180 | 878 bp | At TSS | 189 | |
| chr11:76,782,794–76,784,887 | 1.2 kb | Proximal (<10kb) Multiome | 929 | |
| chr11:76,785,535–76,785,870 | 2.5 kb | Proximal (<10kb) | 52 | |
| chr11:76,787,865–76,789,130 | 5.5 kb | Proximal (<10kb) Multiome | 462 | |
| chr11:76,798,746–76,799,610 | 16.3 kb | Distal (>10kb) Multiome | 661 | |
| chr11:76,807,112–76,807,736 | 24.5 kb | Distal (>10kb) Multiome | 373 | |
| chr11:76,860,430–76,861,513 | 77.8 kb | Distal (>10kb) Multiome | 706 | |
| chr11:77,039,527–77,040,269 | 256.8 kb | Distal (>10kb) Multiome | 214 | |
| chr11:77,066,090–77,067,711 | 283.8 kb | Distal (>10kb) Multiome | 664 |
Genomic view of the TSKU-AS1 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.