Transcription factors with Perturb-seq knockdown data for LINC01556. 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 = LINC01556 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 LINC01556, 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 |
|---|---|---|---|---|
| chr6:28,940,313–28,941,870 | 2.0 kb | Proximal (<10kb) | 807 | |
| chr6:28,943,542–28,944,680 | at TSS | At TSS | 783 | |
| chr6:28,950,970–28,951,262 | 7.1 kb | Proximal (<10kb) | 461 | |
| chr6:28,953,160–28,953,378 | 9.3 kb | Proximal (<10kb) | 566 |
Genomic view of the LINC01556 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.