Motif-editing ExP STARR-seq screen
Compatibility rules of human enhancer and promoter sequencesA focused ExP STARR-seq library tested natural promoter and enhancer sequences together with promoter motif insertions, motif disruptions, and synthetic motif arrays. Edited and unedited constructs were measured in four K562 reporter-RNA replicates and two plasmid-DNA input replicates.
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
Episomal ExP STARR-seq reporter with 264-bp promoter and enhancer inserts. Promoters were edited by inserting GABPA or YY1 motifs or scrambling endogenous motifs; GABPA arrays were also inserted into a control enhancer. The barcode–promoter dictionary used edit-aware sequence matching, and the two DNA input replicates were averaged for activity scoring.
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 · 13 definitions
- promoter_id
- Identifier for the natural or motif-edited 264-bp promoter sequence.
- enhancer_id
- Identifier for the natural, reverse-oriented, scrambled, or synthetic-motif enhancer sequence.
- barcode_count
- Number of barcodes for this promoter–enhancer pair passing mean DNA input ≥25 and four-replicate RNA total ≥1.
- dna_input_mean_sum
- Sum across qualifying barcodes of the mean of eDNA-R1_count and eDNA-R2_count.
- rna_rep1_sum
- Sum of deposited ExP-R1 reporter RNA counts across qualifying barcodes.
- rna_rep2_sum
- Sum of deposited ExP-R2 reporter RNA counts across qualifying barcodes.
- rna_rep3_sum
- Sum of deposited ExP-R3 reporter RNA counts across qualifying barcodes.
- rna_rep4_sum
- Sum of deposited ExP-R4 reporter RNA counts across qualifying barcodes.
- rna_total_sum
- Sum of all four deposited reporter RNA replicate counts across qualifying barcodes.
- activity_log2_mean
- Mean barcode-level log2 RNA/DNA activity, where RNA is the four-replicate RNA total and DNA is the mean of the two DNA input replicates.
- activity_log2_sd
- Population standard deviation of qualifying barcode-level log2 RNA/DNA activities for the pair.
- activity_log2_min
- Minimum qualifying barcode-level log2 RNA/DNA activity for the pair.
- activity_log2_max
- Maximum qualifying barcode-level log2 RNA/DNA activity for the pair.
Quality control
Author QC: edit-aware promoter assignment required a perfect match at edit sites plus flanking bases and at least 90% perfect matching across the assigned sequence; singleton barcode–promoter assignments and ambiguous pairings were removed, and the barcode dictionary required at least five reads. The authors then retained plasmids with more than 25 DNA input reads and more than 1 RNA transcript. For this pair-level table, a barcode passed when the mean of the two deposited DNA input counts was ≥25 and the four-replicate RNA total was ≥1; pairs required at least two qualifying barcodes. The GEO file yielded 370,755 qualifying barcodes and 18,018 pair rows under this reproducible rule, whereas the manuscript reports 362,905 plasmids across 19,019 pairs.
Curation notes
The motif dataset is a targeted mechanistic follow-up to the main ExP screen, not a genome-wide variant-effect assay. Motif edits are encoded in the source promoter/enhancer identifiers; the original counts retain the individual barcodes and both DNA input replicates.