Genome-wide STARR-seq enhancer activity in S2* cells under control, 20E, and IMD conditions
A genome-wide survey reveals that a diverse array of enhancers coordinates the Drosophila innate immune responseA genome-wide Drosophila melanogaster genomic-fragment library was cloned into the pSTARR-seq reporter and electroporated into the hemocyte-like S2* cell line. The transfected population was split into Control, 20E, and IMD arms, each measured in three biological replicates; the processed table summarizes the paper's non-overlapping activity-class enhancer set across all three arms.
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
Control: water then PBS; 20E: 40 nM 20-hydroxyecdysone then PBS; IMD: 40 nM 20-hydroxyecdysone then 0.4 OD heat-killed Serratia marcescens (HKSM)
Male and female iso-1 genomic DNA was sonicated and size-selected at 500–750 bp, cloned by Gibson assembly into the fly pSTARR-seq plasmid (Addgene #71499) with the Drosophila synthetic core promoter, and electroporated into S2* cells. Polyadenylated STARR transcripts were isolated, reverse-transcribed, junction-PCR amplified, and sequenced together with the input plasmid library. STARRPeaker compared output RNA with input DNA and reported log2 normalized output/input activity, input/output fragment coverage, and p/q statistics for each peak.
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 · 47 definitions
- enhancer_id
- Stable identifier constructed from the dm6 assembly and the enhancer's coordinates.
- chrom
- Drosophila chromosome or contig.
- start_0based
- BED start coordinate, 0-based inclusive.
- end_0based_exclusive
- BED end coordinate, 0-based exclusive.
- length_bp
- Length of the non-overlapping activity-class interval in base pairs.
- source_activity_class_code
- Activity-class code copied from GSE308695_Activity_class_all.bed.
- activity_class
- Expanded activity class: Constitutive, Control Only, 20E Only, IMD Only, Control + 20E, Control + IMD, or IMD + 20E.
- control_active
- Whether the activity-class interval is assigned to the Control consensus set.
- twentyE_active
- Whether the activity-class interval is assigned to the 20E consensus set.
- imd_active
- Whether the activity-class interval is assigned to the IMD consensus set.
- control_consensus_count
- Number of Control consensus intervals associated with this activity-class interval under the paper's >=60% overlap rule.
- control_replicate_support
- Number of distinct Control STARR-seq replicate files contributing mapped peak calls.
- control_replicate_ids
- Semicolon-separated GEO sample accessions contributing Control peak calls.
- control_peak_count
- Number of unique Control replicate peak rows used for the summary statistics.
- control_consensus_coordinates
- Associated Control consensus interval(s) as chrom:start-end, using 0-based half-open coordinates.
- control_mean_log2_output_input
- Mean STARRPeaker log2 normalized output/input value across contributing Control peaks.
- control_sd_log2_output_input
- Sample standard deviation of Control contributing-peak log2 normalized output/input values.
- control_mean_starrpeaker_score
- Mean STARRPeaker peak score across contributing Control peaks.
- control_mean_input_fragment_coverage
- Mean input plasmid-library fragment coverage across contributing Control peaks.
- control_mean_output_fragment_coverage
- Mean output STARR transcript fragment coverage across contributing Control peaks.
- control_mean_neglog10_p
- Mean -log10 nominal p-value reported by STARRPeaker for contributing Control peaks.
- control_mean_neglog10_q
- Mean -log10 q-value reported by STARRPeaker for contributing Control peaks.
- twentyE_consensus_count
- Number of 20E consensus intervals associated with this activity-class interval under the paper's >=60% overlap rule.
- twentyE_replicate_support
- Number of distinct 20E STARR-seq replicate files contributing mapped peak calls.
- twentyE_replicate_ids
- Semicolon-separated GEO sample accessions contributing 20E peak calls.
- twentyE_peak_count
- Number of unique 20E replicate peak rows used for the summary statistics.
- twentyE_consensus_coordinates
- Associated 20E consensus interval(s) as chrom:start-end, using 0-based half-open coordinates.
- twentyE_mean_log2_output_input
- Mean STARRPeaker log2 normalized output/input value across contributing 20E peaks.
- twentyE_sd_log2_output_input
- Sample standard deviation of 20E contributing-peak log2 normalized output/input values.
- twentyE_mean_starrpeaker_score
- Mean STARRPeaker peak score across contributing 20E peaks.
- twentyE_mean_input_fragment_coverage
- Mean input plasmid-library fragment coverage across contributing 20E peaks.
- twentyE_mean_output_fragment_coverage
- Mean output STARR transcript fragment coverage across contributing 20E peaks.
- twentyE_mean_neglog10_p
- Mean -log10 nominal p-value reported by STARRPeaker for contributing 20E peaks.
- twentyE_mean_neglog10_q
- Mean -log10 q-value reported by STARRPeaker for contributing 20E peaks.
- imd_consensus_count
- Number of IMD consensus intervals associated with this activity-class interval under the paper's >=60% overlap rule.
- imd_replicate_support
- Number of distinct IMD STARR-seq replicate files contributing mapped peak calls.
- imd_replicate_ids
- Semicolon-separated GEO sample accessions contributing IMD peak calls.
- imd_peak_count
- Number of unique IMD replicate peak rows used for the summary statistics.
- imd_consensus_coordinates
- Associated IMD consensus interval(s) as chrom:start-end, using 0-based half-open coordinates.
- imd_mean_log2_output_input
- Mean STARRPeaker log2 normalized output/input value across contributing IMD peaks.
- imd_sd_log2_output_input
- Sample standard deviation of IMD contributing-peak log2 normalized output/input values.
- imd_mean_starrpeaker_score
- Mean STARRPeaker peak score across contributing IMD peaks.
- imd_mean_input_fragment_coverage
- Mean input plasmid-library fragment coverage across contributing IMD peaks.
- imd_mean_output_fragment_coverage
- Mean output STARR transcript fragment coverage across contributing IMD peaks.
- imd_mean_neglog10_p
- Mean -log10 nominal p-value reported by STARRPeaker for contributing IMD peaks.
- imd_mean_neglog10_q
- Mean -log10 q-value reported by STARRPeaker for contributing IMD peaks.
- qc_pass
- True for every retained activity-class enhancer after author-defined consensus and overlap QC.
Quality control
Author QC was retained: STARRPeaker called peaks per replicate with a p-value threshold below 0.05; the paper reports greater than 0.95 Pearson correlation between replicates within treatment groups; condition-specific consensus enhancers required overlap in at least 2 of 3 biological replicates with at least 1 bp of overlap, using the union of contributing peaks; and activity classes used at least 60% overlap of either condition-specific enhancer. The processed table retains all 4,270 rows from the author-provided Activity_class_all file because each row belongs to one of the seven consensus-derived activity classes and its condition membership agrees with the consensus BED files. Replicate summary values are calculated from unique contributing STARRPeaker peak rows; no additional rows failed QC.
Curation notes
This single experiment represents one transfected genome-wide library split into three STARR-seq treatment arms. GEO sample order is interleaved by biological replicate: GSM9251593/1594/1595 are Control/20E/IMD replicate 1; GSM9251596/1597/1598 are Control/20E/IMD replicate 2; GSM9251599/1600/1601 are Control/20E/IMD replicate 3. The source Activity_class_all file contains 4,270 non-overlapping enhancer intervals in seven classes: 1,344 Constitutive, 748 Control Only, 418 20E Only, 372 IMD Only, 190 Control + 20E, 92 Control + IMD, and 1,106 IMD + 20E. The source IMD consensus BED has inconsistent trailing columns; only its first three BED coordinate fields were used, while all raw source files are preserved unchanged. S2* was mapped to its Schneider 2 parent Cellosaurus entry CVCL_Z232 because no distinct S2* Cellosaurus record was resolved. RNA-seq, ATAC-seq, and raw sequencing-read archive files were not needed for the MPRA/STARR-seq table and were not copied into raw_data.