Transcription factors with Perturb-seq knockdown data for LINC00339. 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 = LINC00339 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 LINC00339, 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 |
|---|---|---|---|---|
| chr1:21,782,310–21,784,177 | 242.1 kb | Distal (>10kb) Multiome | 1096 | |
| chr1:21,814,299–21,814,932 | 210.9 kb | Distal (>10kb) Multiome | 227 | |
| chr1:21,922,465–21,923,180 | 102.7 kb | Distal (>10kb) Multiome | 263 | |
| chr1:21,936,519–21,938,007 | 88.1 kb | Distal (>10kb) Multiome | 630 | |
| chr1:22,024,858–22,026,137 | 27 bp | At TSS Multiome | 937 | |
| chr1:22,052,314–22,053,858 | 27.2 kb | Distal (>10kb) Multiome | 912 | |
| chr1:22,142,284–22,143,888 | 117.9 kb | Distal (>10kb) Multiome | 298 | |
| chr1:22,154,320–22,155,232 | 129.4 kb | Distal (>10kb) Multiome | 103 |
Genomic view of the LINC00339 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.