Transcription factors with Perturb-seq knockdown data for LINC01097. 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 = LINC01097 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 LINC01097, 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 |
|---|---|---|---|---|
| chr4:13,522,245–13,523,548 | 7.9 kb | Proximal (<10kb) | 190 | |
| chr4:13,527,521–13,528,201 | 3.2 kb | Proximal (<10kb) | 104 | |
| chr4:13,529,217–13,529,960 | 1.5 kb | Proximal (<10kb) | 82 | |
| chr4:13,530,965–13,531,852 | at TSS | At TSS | 173 | |
| chr4:13,534,108–13,535,093 | 2.7 kb | Proximal (<10kb) | 79 | |
| chr4:13,535,571–13,536,360 | 4.2 kb | Proximal (<10kb) | 70 | |
| chr4:13,539,011–13,539,477 | 7.6 kb | Proximal (<10kb) | 44 | |
| chr4:13,540,992–13,542,953 | 9.6 kb | Proximal (<10kb) | 321 |
Genomic view of the LINC01097 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.