COF-STAP-seq genome-wide core-promoter screen in Drosophila S2 cells
Transcriptional cofactors display specificity for distinct types of core promotersA 72,000-element Drosophila core-promoter oligonucleotide library was assayed in S2 cells while individual GAL4-DBD-tethered cofactors were recruited to a 4xUAS reporter. Three biological replicates were generated for 23 cofactors plus P65 and GFP controls, and productive reporter initiation was quantified by UMI-collapsed STAP-seq tags.
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
GAL4-DBD-tethered Drosophila cofactor recruitment; P65 positive and GFP negative controls
Episomal promoter/core-promoter MPRA using pSTAP-seq_fly-4xUAS (Addgene 125149). Candidate inserts are 133 bp genomic DNA fragments centered on major TSSs, pooled with Drosophila pseudoobscura spike-in CPs, and co-transfected with GAL4-DBD-cofactor expression plasmids. Reporter RNA was captured with a 5-prime linker containing a 10-nt UMI and sample barcode; paired-end Illumina reads were UMI-collapsed, mapped to candidate oligos, spike-in normalized, and averaged across three biological replicates. Conditions represented in the processed table: 23 Drosophila cofactors (Nejire/P300, Mof, pCAF/Gcn5, Atac2, Tip60, Br140, Lpt, Trr, Trx, Brm, Chro, Brd8, Brd9, fs(1)h/Brd4, MED15, MED24, MED25, Taf4, Tbp, Trf2, EMSY, Gfzf and Pzg), P65, and GFP.
Processed data
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Visible columns (124 of 124)
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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 · 124 definitions
- element_id
- Unique oligonucleotide/core-promoter candidate identifier from the GEO processed table.
- element_type
- Library candidate, synthetic control, or species-specific spike-in control.
- chromosome
- Reference chromosome from the candidate library; blank for synthetic and spike-in controls.
- oligo_start
- Start coordinate of the 133-bp candidate oligo as supplied by the library annotation.
- oligo_end
- End coordinate of the 133-bp candidate oligo as supplied by the library annotation.
- tss
- Major transcription start site coordinate used to center the candidate oligo; blank for controls.
- strand
- Candidate strand from the library annotation.
- supporting_dataset
- Dataset or annotation source supporting inclusion of the candidate TSS.
- genomic_feature
- Library annotation for genomic feature; blank when not supplied for the human library.
- sequence
- 133-bp candidate DNA sequence in the synthesized oligo orientation.
- p65_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for p65, averaged across the available biological replicates.
- nej_p300_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Nej_p300, averaged across the available biological replicates.
- med25_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Med25, averaged across the available biological replicates.
- lpt_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Lpt, averaged across the available biological replicates.
- med15_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Med15, averaged across the available biological replicates.
- cg7154_brd9_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for CG7154_Brd9, averaged across the available biological replicates.
- fs1h_brd4_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for fs1h_Brd4, averaged across the available biological replicates.
- trr_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for trr, averaged across the available biological replicates.
- trx_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for trx, averaged across the available biological replicates.
- gfzf_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for gfzf, averaged across the available biological replicates.
- chro_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Chro, averaged across the available biological replicates.
- cg15356_emsy_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for CG15356_EMSY, averaged across the available biological replicates.
- brd8_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Brd8, averaged across the available biological replicates.
- mof_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Mof, averaged across the available biological replicates.
- taf4_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Taf4, averaged across the available biological replicates.
- trf2_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Trf2, averaged across the available biological replicates.
- med24_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Med24, averaged across the available biological replicates.
- tbp_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Tbp, averaged across the available biological replicates.
- pzg_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for pzg, averaged across the available biological replicates.
- br140_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Br140, averaged across the available biological replicates.
- tip60_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Tip60, averaged across the available biological replicates.
- brm_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for brm, averaged across the available biological replicates.
- atac2_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Atac2, averaged across the available biological replicates.
- pcaf_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for pCAF, averaged across the available biological replicates.
- p65_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for p65, biological replicate 1, from the GEO per-oligo source table.
- p65_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for p65, biological replicate 2, from the GEO per-oligo source table.
- p65_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for p65, biological replicate 3, from the GEO per-oligo source table.
- nej_p300_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Nej_p300, biological replicate 1, from the GEO per-oligo source table.
- nej_p300_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Nej_p300, biological replicate 2, from the GEO per-oligo source table.
- nej_p300_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Nej_p300, biological replicate 3, from the GEO per-oligo source table.
- med25_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Med25, biological replicate 1, from the GEO per-oligo source table.
- med25_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Med25, biological replicate 2, from the GEO per-oligo source table.
- med25_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Med25, biological replicate 3, from the GEO per-oligo source table.
- lpt_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Lpt, biological replicate 1, from the GEO per-oligo source table.
- lpt_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Lpt, biological replicate 2, from the GEO per-oligo source table.
- lpt_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Lpt, biological replicate 3, from the GEO per-oligo source table.
- med15_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Med15, biological replicate 1, from the GEO per-oligo source table.
- med15_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Med15, biological replicate 2, from the GEO per-oligo source table.
- med15_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Med15, biological replicate 3, from the GEO per-oligo source table.
- cg7154_brd9_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for CG7154_Brd9, biological replicate 1, from the GEO per-oligo source table.
- cg7154_brd9_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for CG7154_Brd9, biological replicate 2, from the GEO per-oligo source table.
- cg7154_brd9_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for CG7154_Brd9, biological replicate 3, from the GEO per-oligo source table.
- fs1h_brd4_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for fs1h_Brd4, biological replicate 1, from the GEO per-oligo source table.
- fs1h_brd4_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for fs1h_Brd4, biological replicate 2, from the GEO per-oligo source table.
- fs1h_brd4_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for fs1h_Brd4, biological replicate 3, from the GEO per-oligo source table.
- trr_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for trr, biological replicate 1, from the GEO per-oligo source table.
- trr_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for trr, biological replicate 2, from the GEO per-oligo source table.
- trr_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for trr, biological replicate 3, from the GEO per-oligo source table.
- trx_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for trx, biological replicate 1, from the GEO per-oligo source table.
- trx_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for trx, biological replicate 2, from the GEO per-oligo source table.
- trx_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for trx, biological replicate 3, from the GEO per-oligo source table.
- gfzf_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for gfzf, biological replicate 1, from the GEO per-oligo source table.
- gfzf_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for gfzf, biological replicate 2, from the GEO per-oligo source table.
- gfzf_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for gfzf, biological replicate 3, from the GEO per-oligo source table.
- chro_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Chro, biological replicate 1, from the GEO per-oligo source table.
- chro_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Chro, biological replicate 2, from the GEO per-oligo source table.
- chro_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Chro, biological replicate 3, from the GEO per-oligo source table.
- cg15356_emsy_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for CG15356_EMSY, biological replicate 1, from the GEO per-oligo source table.
- cg15356_emsy_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for CG15356_EMSY, biological replicate 2, from the GEO per-oligo source table.
- cg15356_emsy_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for CG15356_EMSY, biological replicate 3, from the GEO per-oligo source table.
- brd8_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Brd8, biological replicate 1, from the GEO per-oligo source table.
- brd8_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Brd8, biological replicate 2, from the GEO per-oligo source table.
- brd8_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Brd8, biological replicate 3, from the GEO per-oligo source table.
- mof_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Mof, biological replicate 1, from the GEO per-oligo source table.
- mof_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Mof, biological replicate 2, from the GEO per-oligo source table.
- mof_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Mof, biological replicate 3, from the GEO per-oligo source table.
- taf4_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Taf4, biological replicate 1, from the GEO per-oligo source table.
- taf4_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Taf4, biological replicate 2, from the GEO per-oligo source table.
- taf4_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Taf4, biological replicate 3, from the GEO per-oligo source table.
- trf2_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Trf2, biological replicate 1, from the GEO per-oligo source table.
- trf2_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Trf2, biological replicate 2, from the GEO per-oligo source table.
- trf2_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Trf2, biological replicate 3, from the GEO per-oligo source table.
- med24_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Med24, biological replicate 1, from the GEO per-oligo source table.
- med24_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Med24, biological replicate 2, from the GEO per-oligo source table.
- med24_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Med24, biological replicate 3, from the GEO per-oligo source table.
- tbp_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Tbp, biological replicate 1, from the GEO per-oligo source table.
- tbp_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Tbp, biological replicate 2, from the GEO per-oligo source table.
- tbp_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Tbp, biological replicate 3, from the GEO per-oligo source table.
- pzg_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for pzg, biological replicate 1, from the GEO per-oligo source table.
- pzg_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for pzg, biological replicate 2, from the GEO per-oligo source table.
- pzg_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for pzg, biological replicate 3, from the GEO per-oligo source table.
- br140_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Br140, biological replicate 1, from the GEO per-oligo source table.
- br140_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Br140, biological replicate 2, from the GEO per-oligo source table.
- br140_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Br140, biological replicate 3, from the GEO per-oligo source table.
- tip60_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Tip60, biological replicate 1, from the GEO per-oligo source table.
- tip60_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Tip60, biological replicate 2, from the GEO per-oligo source table.
- tip60_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Tip60, biological replicate 3, from the GEO per-oligo source table.
- brm_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for brm, biological replicate 1, from the GEO per-oligo source table.
- brm_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for brm, biological replicate 2, from the GEO per-oligo source table.
- brm_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for brm, biological replicate 3, from the GEO per-oligo source table.
- atac2_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Atac2, biological replicate 1, from the GEO per-oligo source table.
- atac2_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Atac2, biological replicate 2, from the GEO per-oligo source table.
- atac2_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Atac2, biological replicate 3, from the GEO per-oligo source table.
- pcaf_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for pCAF, biological replicate 1, from the GEO per-oligo source table.
- pcaf_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for pCAF, biological replicate 2, from the GEO per-oligo source table.
- pcaf_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for pCAF, biological replicate 3, from the GEO per-oligo source table.
- gfp_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for GFP, biological replicate 1, from the GEO per-oligo source table.
- gfp_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for GFP, biological replicate 2, from the GEO per-oligo source table.
- gfp_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for GFP, biological replicate 3, from the GEO per-oligo source table.
- gfp_rep4_unique_tags
- UMI-collapsed unique reporter-tag count for GFP, biological replicate 4, from the GEO per-oligo source table.
- gfp_rep5_unique_tags
- UMI-collapsed unique reporter-tag count for GFP, biological replicate 5, from the GEO per-oligo source table.
- gfp_rep6_unique_tags
- UMI-collapsed unique reporter-tag count for GFP, biological replicate 6, from the GEO per-oligo source table.
- strongest_activator
- Non-GFP condition with the largest normalized reporter-tag count for this candidate; P65 is included as the positive-control condition.
- strongest_activator_norm_tagcount
- Largest normalized reporter-tag count among non-GFP conditions.
- strongest_activator_over_gfp
- Strongest non-GFP normalized tag count divided by GFP normalized tag count using a 0.5-tag pseudocount in numerator and denominator; derived package metric.
- conditions_over_2x_gfp
- Semicolon-separated non-GFP conditions with pseudocount-adjusted normalized tag count at least twofold above GFP.
- n_conditions_over_2x_gfp
- Number of non-GFP conditions meeting the pseudocount-adjusted twofold-over-GFP criterion.
- max_support_replicates_ge5
- Maximum number of biological replicate columns with at least 5 unique tags for any non-GFP condition.
- support_condition
- Non-GFP condition attaining max_support_replicates_ge5; ties follow normalized-source column order.
- conditions_support_ge5_in_2_reps
- Semicolon-separated non-GFP conditions with at least 5 unique tags in at least 2 biological replicates.
- qc_basis
- QC rule used for row retention: published active set or replicate-support filter.
- published_active_s2
- TRUE when the candidate is in the authors’ 30,936-element S2 activated-CP set (Supplementary Table 11); blank for non-S2 experiments.
- published_nonredundant_s2
- TRUE when the candidate is in the authors’ nonredundant S2 activated-CP set (Supplementary Table 13); blank for non-S2 experiments.
- qc_pass
- TRUE for every row retained in this processed table after the experiment-specific QC filter.
Quality control
The authors retained CPs supported by >=5 unique reporter tags (with >=3 tags supporting a single TSS) in at least 2 replicates, tested each condition against GFP by one-sided Student's t-test with Benjamini-Hochberg correction, and called activation at FDR <=0.06 and fold-change >=2. This table uses the authors' published activated S2 CP set (Supplementary Table 11) as the QC-filtered population: 30,936 of 72,000 source rows retained and 41,064 excluded. The GEO source is aggregated per oligo, so the single-TSS support subcriterion cannot be independently rechecked here.
Curation notes
Source GEO accession: GSE116197. The GEO S2 unique-count file contains six GFP replicate columns (GFP_Rep1-6) and a nonstandard Tip60 replicate order; all source columns are retained with stable replicate numbering in the processed table. The S2 table is restricted to the authors' 30,936 activated CPs in Supplementary Table 11; the authors' 25,971-element nonredundant subset is exposed as a flag. Aggregate per-oligo counts cannot independently verify the paper's >=3-tags-at-one-TSS subcriterion. The processed table retains the authors' 30,936 activated CPs (Supplementary Table 11); 25,971 are also in their nonredundant Supplementary Table 13 set. Normalized activity values are reporter-tag counts rather than RNA/DNA ratios because STAP-seq reports productive initiation from the promoter library and does not use a DNA-input denominator in the deposited processed table.