BG3-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 neuronal ML-DmBG3-c2 cells using the self-transcribing active regulatory region reporter. The processed table contains final STARR-seq peak calls, GEO peak P-values, 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; BG3 was assayed in two paired-end biological replicates with respective inputs. Cells were cultured in M3 BPYE medium with 10% FCS, 10 micrograms/mL insulin, and 1% penicillin/streptomycin at 25 degrees C, and the plasmid library was introduced by electroporation.
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 BG3 STARR-seq peak.
- cell_type
- Drosophila cell line condition represented by the row; BG3 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
- GEO processed BG3 peak P-value copied from GSE49809_BG3_Dmel_DSCP_500bp.peaks.txt.
- 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 BG3 summit is within less than 500 bp of a published S2-centered Broad enhancer summit; this is a transparent nearest-summit cross-cell join and is not a one-to-one remapping.
- 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 BG3 peak (BG3-specific or a nearby Broad region); blank for peaks outside the 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 BG3 STARR-seq peak calls after requiring a nonmissing dm3 chromosome, integer summit position, finite log2 enrichment, finite GEO peak P-value, and unique chromosome/summit coordinates. No rows were removed: all 4,245 source peaks passed these checks. The GEO processed BG3 file matches the lab aggregate file at all 4,245 coordinates and activity values; its P-values are copied into the table. The paper's peak-calling pipeline had already applied its read-density and hypergeometric significance procedure, so no additional arbitrary activity cutoff was imposed. The table uses the paper's 401-bp summit-centered window and joins the published class labels.
Curation notes
The aggregate BG3 file contains 4,245 peaks and has no exact duplicate coordinates; all rows passed package QC. The aggregate file matches GSE49809's processed peak file at every coordinate and activity value, and the table adds the GEO P-values. The BG3-specific class file contains 499 data rows (header excluded), although the manuscript describes selecting 500 enhancers. Broad.txt is centered on S2 peak summits; 480 BG3 aggregate peaks fall within <500 bp of a published Broad summit, and the table records the nearest S2 summit and distance. The BG3 sequencing series is GSE49809 / BioProject PRJNA214972.