Transcription factors with Perturb-seq knockdown data for LINC01609. 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 = LINC01609 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 LINC01609, 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 |
|---|---|---|---|---|
| chr8:111,229,181–111,229,759 | 6.4 kb | Proximal (<10kb) | 49 | |
| chr8:111,229,884–111,230,200 | 6.0 kb | Proximal (<10kb) | 10 | |
| chr8:111,236,031–111,236,853 | at TSS | At TSS | 196 | |
| chr8:111,241,965–111,242,131 | 5.8 kb | Proximal (<10kb) | 4 | |
| chr8:111,242,256–111,242,386 | 6.1 kb | Proximal (<10kb) | 3 |
Genomic view of the LINC01609 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.