SuRE23 genome-wide autonomous promoter activity in K562
Genome-wide mapping of autonomous promoter activity in human cellsA genome-wide library of randomly sheared human genomic fragments (approximately 0.2-2 kb) was cloned upstream of a promoter-less reporter transcription unit containing a random 20-bp barcode and transiently transfected into K562 erythroleukemia cells. The processed table contains the authors' called SuRE autonomous-promoter peaks and their genomic feature annotations.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Basal / untreated
SuRE (Survey of Regulatory Elements) is an episomal plasmid barcode reporter assay. Random human genomic fragments were cloned upstream of a promoter-less GFP transcription unit with a random 20-bp barcode; RNA barcode counts were measured after transient transfection and normalized to plasmid input. Fragment orientation is retained, so the assay reports autonomous promoter activity in both directions rather than allele-specific effects.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 15 definitions
- peak_id
- Unique MACS2 SuRE peak identifier from the authors' supplementary dataset
- chromosome
- hg19 chromosome containing the peak
- start
- Zero-based genomic start coordinate of the peak interval as released
- end
- Genomic end coordinate of the peak interval as released
- summit
- MACS2 peak summit coordinate
- peak_width_bp
- Peak interval width in base pairs, calculated as end - start
- macs2_score
- MACS2 peak score from the authors' peak call
- sure_score_fold_enrichment
- Mean SuRE signal/fold enrichment across the peak interval
- log2_sure_score
- Base-2 logarithm of sure_score_fold_enrichment, calculated for packaging
- tss_overlap_count
- Number of annotated TSS regions overlapping the peak summit
- enhancer_overlap_count
- Number of annotated enhancer regions overlapping the peak summit
- repeat_overlap_count
- Number of RepeatMasker/repetitive sequence regions overlapping the peak summit
- repeat_family
- Repeat family annotation when a repeat overlaps the summit; blank when none was reported
- repeat_name
- Repeat name annotation when a repeat overlaps the summit; blank when none was reported
- annotation_category
- Semicolon-separated summary of TSS, enhancer, repeat, or unannotated/other overlap
Quality control
Paper-reported QC was used: barcode-to-fragment associations were generated by paired-end iPCR mapping to hg19, reads with invalid barcode/mapping characteristics were removed, barcodes associated with multiple genomic positions were filtered, and duplicate-position barcode errors were aggregated. The authors called peaks with MACS2 at FDR <= 0.05 and retained peaks with at least 2-fold SuRE enrichment. The released source table contains 55,453 rows and every retained row has SuRE.score >= 2; no additional peak rows were removed during packaging.
Curation notes
This is a promoter-focused SuRE MPRA study rather than a variant-contrast experiment: the table reports genomic peak activity and annotations, not rsIDs or alternative alleles. The genome-wide experiment used the SuRE23 library and two independent biological replicates in K562 cells; the peak table is the authors' integrated call across those replicates. The large barcode-level GEO archive and BigWig tracks were omitted from raw_data because the compact released peak table is sufficient for this package.