Transcription factors with Perturb-seq knockdown data for NEGR1-IT1. 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 = NEGR1-IT1 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 NEGR1-IT1, 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 |
|---|---|---|---|---|
| chr1:71,828,574–71,828,923 | 8.1 kb | Proximal (<10kb) | 17 | |
| chr1:71,836,749–71,837,402 | at TSS | At TSS | 13 | |
| chr1:71,845,428–71,846,108 | 8.4 kb | Proximal (<10kb) | 7 |
Genomic view of the NEGR1-IT1 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.