Transcription factors with Perturb-seq knockdown data for LINC01096. 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 = LINC01096 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 LINC01096, 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 |
|---|---|---|---|---|
| chr4:13,539,011–13,539,477 | 8.3 kb | Proximal (<10kb) | 44 | |
| chr4:13,540,992–13,542,953 | 4.8 kb | Proximal (<10kb) | 321 | |
| chr4:13,543,269–13,545,468 | 2.3 kb | Proximal (<10kb) | 614 | |
| chr4:13,546,533–13,548,322 | at TSS | At TSS | 466 | |
| chr4:13,548,795–13,549,621 | 994 bp | At TSS | 388 |
Genomic view of the LINC01096 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.