Genome-wide STAP-seq zfh1 enhancer responsiveness in Drosophila S2 cells
Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolutionRandomly sheared Drosophila genomic fragments were cloned at the core-promoter position of an episomal reporter between the zfh1 enhancer and reporter ORF, with a matched enhancerless construct used to measure basal activity. Polyadenylated reporter transcripts were cap-enriched, UMI-counted, and mapped strand-specifically to identify transcription initiation at single-base-pair resolution.
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
Defined zfh1 developmental enhancer present versus enhancerless control
STAP-seq measures sequence-intrinsic core-promoter responsiveness to a fixed enhancer and is complementary to STARR-seq. The pGL3-derived reporter carried 100–250-bp genomic fragments, an mhc16 intron, truncated sgGFP ORF, and SV40 polyadenylation signal; genome-wide libraries included Drosophila pseudoobscura spike-in plasmids for normalization. Reporter RNA 5′ tags contained an 8-nt UMI, and the paper reported two highly concordant genome-wide zfh1 and enhancerless replicates.
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 · 10 definitions
- element_id
- Author-assigned eTSS identifier (TSS_num).
- chromosome
- Drosophila dm3 chromosome or chromosome arm for the eTSS.
- start
- 0-based inclusive genomic start coordinate from the author-supplied BED-like file.
- end
- 0-based exclusive genomic end coordinate; one base for the called +1 position.
- tss_position_1based
- 1-based genomic coordinate corresponding to the called transcription-initiation position.
- strand
- Strand of the reporter transcription-initiation event.
- zfh1_tag_count
- Author-supplied unique-UMI tag count at the +1 position in the zfh1-enhancer screen.
- ctrl_tag_count
- Author-supplied unique-UMI tag count at the +1 position in the enhancerless control screen.
- enhancer_responsiveness
- Author-supplied spike-in-normalized zfh1/control enhancer-responsiveness score.
- log2_enhancer_responsiveness
- Base-2 logarithm of the author-supplied enhancer-responsiveness score, added for convenient effect-size analysis.
Quality control
The authors trimmed paired-end reads to 44 bp, used the first 8 bp as UMIs, mapped the remaining 36 bp to dm3 and dp3, removed UMIs containing N, collapsed identical UMIs and UMIs differing by one base at the same mapped position, and used spike-in tags for normalization. Published eTSS calling required at least 5 zfh1 tags, greater than 1.5-fold spike-in-corrected zfh1/control enrichment, and P ≤ 0.05; calls within ±10 bp were merged and the highest-responsiveness position retained. The source table contains 13,218 rows that pass the authors' published eTSS/QC selection; no additional rows were retained or removed.
Curation notes
This is the main quantitative genome-wide STAP-seq experiment. Coordinates are dm3 BED-style coordinates, and all rows are the authors' merged eTSS calls rather than unfiltered genomic positions. The count fields are unique-UMI tag counts; the responsiveness field is the authors' normalized score and should not be recalculated from the two displayed count columns alone because spike-in normalization is not fully represented in this table. S2 denotes the Schneider 2 Drosophila cell line (Cellosaurus CVCL_Z232).