Transcription factors with Perturb-seq knockdown data for LINC01355. 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 = LINC01355 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 LINC01355, 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 |
|---|---|---|---|---|
| chr1:23,019,210–23,020,140 | 268.1 kb | Distal (>10kb) Multiome | 1023 | |
| chr1:23,168,432–23,169,217 | 118.7 kb | Distal (>10kb) Multiome | 673 | |
| chr1:23,177,510–23,178,128 | 109.7 kb | Distal (>10kb) Multiome | 628 | |
| chr1:23,216,791–23,217,828 | 70.4 kb | Distal (>10kb) Multiome | 415 | |
| chr1:23,343,731–23,344,999 | 57.0 kb | Distal (>10kb) Multiome | 939 | |
| chr1:23,367,863–23,369,864 | 80.9 kb | Distal (>10kb) Multiome | 1018 | |
| chr1:23,370,752–23,371,596 | 83.6 kb | Distal (>10kb) Multiome | 344 | |
| chr1:23,403,774–23,404,231 | 116.5 kb | Distal (>10kb) Multiome | 536 | |
| chr1:23,436,460–23,437,402 | 149.4 kb | Distal (>10kb) Multiome | 248 | |
| chr1:23,483,306–23,485,071 | 196.9 kb | Distal (>10kb) Multiome | 659 | |
| chr1:23,530,568–23,531,711 | 243.8 kb | Distal (>10kb) Multiome | 775 | |
| chr1:23,539,704–23,540,280 | 252.5 kb | Distal (>10kb) Multiome | 668 | |
| chr1:23,554,367–23,556,627 | 267.5 kb | Distal (>10kb) Multiome | 961 | |
| chr1:23,558,135–23,559,925 | 272.1 kb | Distal (>10kb) Multiome | 932 |
Genomic view of the LINC01355 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.