Transcription factors with Perturb-seq knockdown data for LINC03009. 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 = LINC03009 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 LINC03009, 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 |
|---|---|---|---|---|
| chr7:76,259,707–76,261,052 | 289.0 kb | Distal (>10kb) Multiome | 332 | |
| chr7:76,267,044–76,267,853 | 282.0 kb | Distal (>10kb) Multiome | 211 | |
| chr7:76,282,299–76,283,220 | 266.7 kb | Distal (>10kb) Multiome | 237 | |
| chr7:76,291,428–76,292,275 | 257.5 kb | Distal (>10kb) Multiome | 767 | |
| chr7:76,302,207–76,304,173 | 246.8 kb | Distal (>10kb) Multiome | 943 | |
| chr7:76,314,028–76,314,686 | 235.0 kb | Distal (>10kb) Multiome | 715 | |
| chr7:76,317,523–76,319,173 | 231.2 kb | Distal (>10kb) Multiome | 840 | |
| chr7:76,358,237–76,359,989 | 190.1 kb | Distal (>10kb) Multiome | 1036 | |
| chr7:76,379,650–76,380,602 | 169.3 kb | Distal (>10kb) Multiome | 853 | |
| chr7:76,392,882–76,394,121 | 156.1 kb | Distal (>10kb) Multiome | 932 | |
| chr7:76,395,928–76,396,741 | 153.2 kb | Distal (>10kb) Multiome | 152 | |
| chr7:76,397,187–76,397,970 | 151.8 kb | Distal (>10kb) Multiome | 496 | |
| chr7:76,409,261–76,409,956 | 139.6 kb | Distal (>10kb) Multiome | 281 | |
| chr7:76,510,075–76,510,721 | 39.0 kb | Distal (>10kb) Multiome HiCAR | 201 | |
| chr7:76,548,975–76,549,826 | 85 bp | At TSS Multiome | 505 |
Genomic view of the LINC03009 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.