Transcription factors with Perturb-seq knockdown data for CCDC60. 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 = CCDC60 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 CCDC60, 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 |
|---|---|---|---|---|
| chr12:119,068,638–119,069,299 | 265.6 kb | Distal (>10kb) Multiome | 39 | |
| chr12:119,089,271–119,089,712 | 245.3 kb | Distal (>10kb) Multiome | 81 | |
| chr12:119,090,372–119,091,307 | 243.8 kb | Distal (>10kb) Multiome | 53 | |
| chr12:119,153,337–119,154,993 | 181.0 kb | Distal (>10kb) Multiome | 247 | |
| chr12:119,178,270–119,179,483 | 156.2 kb | Distal (>10kb) Multiome | 281 | |
| chr12:119,328,221–119,328,413 | 6.3 kb | Proximal (<10kb) | 35 | |
| chr12:119,334,510–119,334,827 | at TSS | At TSS | 136 | |
| chr12:119,338,807–119,339,255 | 4.4 kb | Proximal (<10kb) Multiome | 45 | |
| chr12:119,486,646–119,487,242 | 152.2 kb | Distal (>10kb) Multiome | 69 |
Genomic view of the CCDC60 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.