Transcription factors with Perturb-seq knockdown data for MSC-AS1. 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 = MSC-AS1 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 MSC-AS1, 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 |
|---|---|---|---|---|
| chr8:71,547,135–71,548,410 | 280.5 kb | Distal (>10kb) Multiome | 321 | |
| chr8:71,651,940–71,652,569 | 176.0 kb | Distal (>10kb) Multiome | 151 | |
| chr8:71,671,847–71,672,784 | 155.8 kb | Distal (>10kb) Multiome | 123 | |
| chr8:71,674,695–71,676,017 | 152.9 kb | Distal (>10kb) Multiome | 64 | |
| chr8:71,687,309–71,688,683 | 139.9 kb | Distal (>10kb) Multiome | 165 | |
| chr8:71,706,258–71,707,055 | 121.5 kb | Distal (>10kb) Multiome | 124 | |
| chr8:71,715,807–71,716,840 | 111.8 kb | Distal (>10kb) Multiome | 170 | |
| chr8:71,827,762–71,828,494 | at TSS | At TSS | 288 | |
| chr8:71,841,631–71,842,524 | 13.9 kb | Distal (>10kb) Multiome | 218 | |
| chr8:71,843,237–71,844,888 | 15.9 kb | Distal (>10kb) Multiome | 479 | |
| chr8:71,845,521–71,845,995 | 1.5 kb | Proximal (<10kb) | 69 | |
| chr8:72,004,121–72,005,732 | 177.1 kb | Distal (>10kb) Multiome HiCAR | 364 | |
| chr8:72,040,280–72,041,455 | 212.5 kb | Distal (>10kb) Multiome | 108 | |
| chr8:72,075,016–72,075,959 | 247.4 kb | Distal (>10kb) Multiome | 217 | |
| chr8:72,134,114–72,134,981 | 306.3 kb | Distal (>10kb) Multiome | 282 |
Genomic view of the MSC-AS1 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.