Transcription factors with Perturb-seq knockdown data for LINC01230. 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 = LINC01230 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 LINC01230, 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 |
|---|---|---|---|---|
| chr9:1,042,136–1,042,263 | 3.4 kb | Proximal (<10kb) | 18 | |
| chr9:1,042,373–1,043,175 | 2.4 kb | Proximal (<10kb) | 123 | |
| chr9:1,045,246–1,045,924 | at TSS | At TSS | 77 | |
| chr9:1,046,106–1,046,417 | 482 bp | At TSS | 34 | |
| chr9:1,046,882–1,047,502 | 1.3 kb | Proximal (<10kb) | 81 | |
| chr9:1,047,595–1,047,729 | 2.0 kb | Proximal (<10kb) | 57 | |
| chr9:1,049,926–1,050,805 | 4.3 kb | Proximal (<10kb) | 331 | |
| chr9:1,051,400–1,052,355 | 5.8 kb | Proximal (<10kb) | 259 | |
| chr9:1,052,464–1,052,615 | 6.8 kb | Proximal (<10kb) | 23 |
Genomic view of the LINC01230 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.