Approximately 500-bp sheared Drosophila melanogaster genomic fragments were cloned into self-transcribing STARR-seq reporters carrying RpS12, DSCP, eEF1delta, x16, NipB, or pnr core promoters and screened in S2 cells. The table contains author-called peak summits and input-normalized activities from the six deposited genome-wide promoter contexts; RpS12 and DSCP are merged two-replicate screens, while several additional contexts have only one deposited peak file.
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.
Organism
Fruit fly
Taxonomy ID
NCBITaxon:7227
Biosample
CVCL:Z232
Reference genome
dm3
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal plasmid STARR-seq reporter in which cloned genomic candidate fragments are assayed through their presence in self-transcribed reporter RNA. Core-promoter sequence was the main construct variable (RpS12/hkCP, DSCP/dCP, eEF1delta, x16, NipB, or pnr); libraries were prepared from whole-genome sheared DNA and sequenced by paired-end Illumina HiSeq 2000. The table reports the deposited peak enrichment over input and author peak-call p-value, with a derived log2 enrichment score.
Processed data
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Visible columns (17 of 17)
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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 identifier composed of cell type, core promoter, chromosome, and reported summit.
core_promoter
Core-promoter sequence carried by the STARR-seq reporter.
cell_type
Drosophila cell context; S2 for this experiment.
library_scope
Genome-wide sheared-genomic-DNA library.
chromosome
dm3 chromosome or heterochromatin contig from the deposited peak call.
summit
Peak summit coordinate as reported in the GEO file.
peak_window_501bp_start
Start of the reported-coordinate +/-250-bp window used for the paper's 501-bp specificity comparison.
peak_window_501bp_end
End of the reported-coordinate +/-250-bp window used for the paper's 501-bp specificity comparison.
enrichment_over_input
Author-deposited STARR-seq enrichment over input at the peak summit.
log2_enrichment_over_input
Derived log2 of enrichment_over_input.
p_value
Author peak-call p-value from the input comparison; zero denotes underflow in the source file.
specificity_class_vs_RpS12_DSCP
For RpS12 and DSCP rows, hkCP-specific, dCP-specific, or shared using the paper's 501-bp summit-window rule; not_assessed for other promoters.
bac_id
Blank because this is the genome-wide library, not the focused BAC library.
replicate_status
Whether the source row comes from a merged replicate set or a single deposited peak file.
source_accession
GEO series and sample accession provenance for the source peak file.
source_file
Relative path to the compressed source peak file in raw_data.
qc_status
Packaging QC result; all retained rows are pass.
Quality control
The authors mapped uniquely to dm3, excluded chrU/chrUextra/chrM, removed clustered or redundant fragments, called peaks against input with hypergeometric tests, and merged biological replicates where provided. For packaging, rows were retained only when they had exactly four tab-separated fields, a chromosome-like dm3 coordinate, an integer summit >=1, finite positive enrichment, and a finite p-value in [0,1]; p=0 was retained as numerical underflow. All 36,886 deposited peak rows passed these checks and no rows were rejected; no new peak calling was performed.
Curation notes
S2 is the Schneider 2 cell line (Cellosaurus CVCL:Z232). The DSCP rows are the paper's reanalysis of the earlier GSE40739 dCP screen; the compact GSE40739 archive and extracted dCP peaks are retained in raw_data for provenance. The source files available for secondary promoter contexts are eEF1delta rep1, x16 rep2, NipB rep2, and a single pnr sample, so those rows must not be interpreted as replicate means. Hsp70 was used by the paper and is represented in the focused BAC table, but no compact genome-wide Hsp70 peak file was deposited in GSE57876. Derived specificity counts are 4,137 hkCP-specific, 3,586 dCP-specific, and 3,641 shared rows, matching Supplementary Table 1's reported specific-peak counts.