Transcription factors with Perturb-seq knockdown data for LINC01011. 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 = LINC01011 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 LINC01011, 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 |
|---|---|---|---|---|
| chr6:2,980,019–2,980,493 | 8.2 kb | Proximal (<10kb) | 252 | |
| chr6:2,984,790–2,985,243 | 3.4 kb | Proximal (<10kb) | 130 | |
| chr6:2,985,539–2,987,671 | 975 bp | At TSS | 402 | |
| chr6:2,987,802–2,990,098 | at TSS | At TSS | 1173 | |
| chr6:2,990,284–2,991,348 | 1.6 kb | Proximal (<10kb) | 509 | |
| chr6:2,998,292–2,998,512 | 9.6 kb | Proximal (<10kb) | 80 |
Genomic view of the LINC01011 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.