Transcription factors with Perturb-seq knockdown data for LINC01234. 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 = LINC01234 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 LINC01234, 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 |
|---|---|---|---|---|
| chr12:113,477,415–113,477,998 | 296.1 kb | Distal (>10kb) Multiome | 71 | |
| chr12:113,514,969–113,515,472 | 258.4 kb | Distal (>10kb) Multiome | 83 | |
| chr12:113,587,617–113,588,195 | 185.8 kb | Distal (>10kb) Multiome | 140 | |
| chr12:113,609,843–113,610,459 | 163.5 kb | Distal (>10kb) Multiome | 80 | |
| chr12:113,778,849–113,779,169 | 5.2 kb | Proximal (<10kb) | 41 | |
| chr12:113,965,897–113,966,787 | 192.7 kb | Distal (>10kb) Multiome | 723 |
Genomic view of the LINC01234 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.