Transcription factors with Perturb-seq knockdown data for LINC00294. 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 = LINC00294 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 LINC00294, 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 |
|---|---|---|---|---|
| chr11:32,829,540–32,830,458 | 246.3 kb | Distal (>10kb) Multiome | 566 | |
| chr11:32,891,344–32,894,653 | 183.2 kb | Distal (>10kb) Multiome | 1040 | |
| chr11:33,015,524–33,016,542 | 60.2 kb | Distal (>10kb) Multiome | 837 | |
| chr11:33,038,936–33,040,258 | 36.7 kb | Distal (>10kb) Multiome | 917 | |
| chr11:33,040,776–33,041,667 | 34.9 kb | Distal (>10kb) Multiome | 161 | |
| chr11:33,049,426–33,050,404 | 26.2 kb | Distal (>10kb) Multiome | 103 | |
| chr11:33,160,986–33,162,028 | 85.4 kb | Distal (>10kb) Multiome | 908 | |
| chr11:33,256,736–33,259,047 | 182.4 kb | Distal (>10kb) Multiome | 993 | |
| chr11:33,375,703–33,377,039 | 300.2 kb | Distal (>10kb) Multiome | 329 |
Genomic view of the LINC00294 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.