COF-STAP-seq core-promoter validation screen in Drosophila Kc167 cells
Transcriptional cofactors display specificity for distinct types of core promotersThe shared 72,000-element Drosophila core-promoter library was assayed in Drosophila Kc167 cells with GAL4-DBD recruitment of six cofactors, P65, and GFP. Each condition was measured in three biological replicates by UMI-collapsed STAP-seq.
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 cofactor recruitment; P65 positive and GFP negative controls
Episomal promoter/core-promoter MPRA using the STAP-seq reporter system and GAL4-DBD recruitment. The 133 bp candidate fragments were pooled with Drosophila pseudoobscura spike-in CPs, reporter RNAs were captured with UMI/sample-barcoded 5-prime linkers, and normalized tag counts were averaged across three biological replicates. Conditions represented in the processed table: MED25, Nejire/P300, Lpt, Gfzf, Chro, Mof, P65, and GFP.
Processed data
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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 · 53 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.
- kc167_p65_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_p65, averaged across the available biological replicates.
- kc167_med25_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_Med25, averaged across the available biological replicates.
- kc167_nej_p300_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_Nej_p300, averaged across the available biological replicates.
- kc167_lpt_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_Lpt, averaged across the available biological replicates.
- kc167_gfzf_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_gfzf, averaged across the available biological replicates.
- kc167_chro_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_Chro, averaged across the available biological replicates.
- kc167_mof_norm_tagcount
- Spike-in-normalized mean unique STAP-seq reporter-tag count for Kc167_Mof, averaged across the available biological replicates.
- kc167_p65_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_p65, biological replicate 1, from the GEO per-oligo source table.
- kc167_p65_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_p65, biological replicate 2, from the GEO per-oligo source table.
- kc167_p65_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_p65, biological replicate 3, from the GEO per-oligo source table.
- kc167_med25_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Med25, biological replicate 1, from the GEO per-oligo source table.
- kc167_med25_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Med25, biological replicate 2, from the GEO per-oligo source table.
- kc167_med25_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Med25, biological replicate 3, from the GEO per-oligo source table.
- kc167_nej_p300_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Nej_p300, biological replicate 1, from the GEO per-oligo source table.
- kc167_nej_p300_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Nej_p300, biological replicate 2, from the GEO per-oligo source table.
- kc167_nej_p300_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Nej_p300, biological replicate 3, from the GEO per-oligo source table.
- kc167_lpt_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Lpt, biological replicate 1, from the GEO per-oligo source table.
- kc167_lpt_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Lpt, biological replicate 2, from the GEO per-oligo source table.
- kc167_lpt_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Lpt, biological replicate 3, from the GEO per-oligo source table.
- kc167_gfzf_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_gfzf, biological replicate 1, from the GEO per-oligo source table.
- kc167_gfzf_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_gfzf, biological replicate 2, from the GEO per-oligo source table.
- kc167_gfzf_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_gfzf, biological replicate 3, from the GEO per-oligo source table.
- kc167_chro_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Chro, biological replicate 1, from the GEO per-oligo source table.
- kc167_chro_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Chro, biological replicate 2, from the GEO per-oligo source table.
- kc167_chro_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Chro, biological replicate 3, from the GEO per-oligo source table.
- kc167_mof_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Mof, biological replicate 1, from the GEO per-oligo source table.
- kc167_mof_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Mof, biological replicate 2, from the GEO per-oligo source table.
- kc167_mof_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_Mof, biological replicate 3, from the GEO per-oligo source table.
- kc167_gfp_rep1_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_GFP, biological replicate 1, from the GEO per-oligo source table.
- kc167_gfp_rep2_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_GFP, biological replicate 2, from the GEO per-oligo source table.
- kc167_gfp_rep3_unique_tags
- UMI-collapsed unique reporter-tag count for Kc167_GFP, biological replicate 3, 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 used UMI-collapsed triplicate STAP-seq counts and spike-in normalization. Because no condition-specific activated-CP table was deposited for this validation screen, this package applied the available row-level portion of the authors' support filter: at least 5 unique tags in at least 2 of 3 biological replicates for at least one non-GFP condition (P65 included as the positive control). The aggregate GEO table does not permit independent verification of the >=3-tags-at-one-TSS or Student's t-test/FDR components. 29,788 of 72,000 source rows retained and 42,212 excluded.
Curation notes
Source GEO accession: GSE116197. No author-defined activated-CP table was provided for Kc167, so the available row-level portion of the published support filter was applied. 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.