S2-cell genome-wide STARR-seq enhancer activity screen
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer featuresA genome-wide approximately 500-bp Drosophila melanogaster genomic-fragment library was assayed episomally in Schneider 2 cells using the self-transcribing active regulatory region reporter. The processed table contains final STARR-seq peak calls, log2 cDNA/input enrichment, and the paper's stringent enhancer-class membership.
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 STARR-seq used a genome-wide Drosophila genomic-fragment library of approximately 500 bp cloned into a pGL3-Promoter-derived reporter carrying the Drosophila Synthetic Core Promoter, sgGFP ORF, and polyadenylation signal. Candidate fragments were transcribed as part of reporter RNA and activity was quantified as log2 enrichment of cDNA fragments over plasmid/input; the source GSE40739 S2 experiment had two paired-end biological replicates and respective inputs.
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 · 17 definitions
- element_id
- Stable package identifier assigned in source-file order to an aggregate S2 STARR-seq peak.
- cell_type
- Drosophila cell line condition represented by the row; S2 for every row.
- chromosome
- dm3 chromosome from the author-supplied peak-summit file.
- summit_position
- Author-supplied STARR-seq peak summit coordinate, copied without modification.
- window_start_0based
- Derived start of the paper's 401-bp summit-centered window, using summit_position minus 200 under a 0-based half-open convention.
- window_end_0based_exclusive
- Derived exclusive end of the 401-bp summit-centered window, using summit_position plus 201 under a 0-based half-open convention.
- log2_enrichment_over_input
- Author-supplied STARR_enrichment value; GEO describes this peak activity value as log2 enrichment over input.
- peak_p_value
- Aggregate peak P-value; blank because the S2 aggregate peak-summit file does not provide one.
- s2_specific_class
- TRUE when the row's chromosome/summit exactly matches the published S2-specific enhancer list; otherwise FALSE.
- bg3_specific_class
- TRUE when the row's chromosome/summit exactly matches the published BG3-specific enhancer list; otherwise FALSE.
- osc_specific_class
- TRUE when the row's chromosome/summit exactly matches the published OSC-specific enhancer list; otherwise FALSE.
- broad_class
- TRUE when the row's summit is within less than 500 bp of a published S2-centered Broad enhancer summit; for S2 rows this is an exact match.
- broad_s2_summit
- Nearest published Broad enhancer summit on the same chromosome when broad_class is TRUE; blank otherwise.
- broad_s2_distance_bp
- Absolute distance in bp from summit_position to broad_s2_summit; blank when broad_class is FALSE.
- paper_enhancer_class
- Published class label for the current S2 peak (S2-specific or Broad); blank for peaks outside the four stringent class sets.
- source_peak_file
- Raw-data filename containing the aggregate peak row.
- qc_pass
- TRUE for rows retained after package-level structural QC.
Quality control
Retained the authors' final aggregate S2 STARR-seq peak calls after requiring a nonmissing dm3 chromosome, integer summit position, finite log2 enrichment, and unique chromosome/summit coordinates. No rows were removed: all 5,499 source peaks passed these structural checks. The paper's peak-calling pipeline supplied the source calls, while the two replicate peak-call files are preserved in raw_data and were not re-called. The table uses the paper's 401-bp summit-centered window and joins published class labels; no arbitrary enrichment cutoff was applied because the stringent class definitions also use peak P-values that are not present in the aggregate S2 file.
Curation notes
The aggregate S2 file contains 5,499 peaks and has no exact duplicate coordinates; all rows passed package QC. The source S2-specific and Broad class files each contain 499 data rows (header excluded), although the manuscript describes selecting 500 enhancers. Broad.txt is authoritative for the S2-centered broad set, and the S2 table therefore has 499 exact broad flags. S2 and OSC activity maps were originally generated in the earlier GSE40739 study and reused here; the four relevant GSE40739 STARR-seq replicate peak-call files are included in raw_data.