A 12,000-element representative human promoter/enhancer/control oligonucleotide library was assayed in HCT116 cells with GAL4-DBD recruitment of five human 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.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0291
Reference genome
hg19
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
GAL4-DBD-tethered human cofactor recruitment; P65 positive and GFP negative controls
Episomal promoter/core-promoter MPRA using pSTAP-seq_human-4xUAS (Addgene 125150) with GAL4-DBD recruitment. The 133 bp human candidate fragments were selected from promoter, enhancer, and control classes, pooled with mouse promoter spike-ins, and reporter RNAs were UMI/sample-barcoded, sequenced, spike-in normalized, and averaged across three biological replicates. Conditions represented in the processed table: MED15, BRD4, EP300, MLL3, EMSY, 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 · 49 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.
med15_norm_tagcount
Spike-in-normalized mean unique STAP-seq reporter-tag count for MED15, averaged across the available biological replicates.
brd4_norm_tagcount
Spike-in-normalized mean unique STAP-seq reporter-tag count for BRD4, averaged across the available biological replicates.
ep300_norm_tagcount
Spike-in-normalized mean unique STAP-seq reporter-tag count for EP300, averaged across the available biological replicates.
mll3_norm_tagcount
Spike-in-normalized mean unique STAP-seq reporter-tag count for MLL3, averaged across the available biological replicates.
emsy_norm_tagcount
Spike-in-normalized mean unique STAP-seq reporter-tag count for EMSY, 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.
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.
brd4_rep1_unique_tags
UMI-collapsed unique reporter-tag count for BRD4, biological replicate 1, from the GEO per-oligo source table.
brd4_rep2_unique_tags
UMI-collapsed unique reporter-tag count for BRD4, biological replicate 2, from the GEO per-oligo source table.
brd4_rep3_unique_tags
UMI-collapsed unique reporter-tag count for BRD4, biological replicate 3, from the GEO per-oligo source table.
ep300_rep1_unique_tags
UMI-collapsed unique reporter-tag count for EP300, biological replicate 1, from the GEO per-oligo source table.
ep300_rep2_unique_tags
UMI-collapsed unique reporter-tag count for EP300, biological replicate 2, from the GEO per-oligo source table.
ep300_rep3_unique_tags
UMI-collapsed unique reporter-tag count for EP300, biological replicate 3, from the GEO per-oligo source table.
mll3_rep1_unique_tags
UMI-collapsed unique reporter-tag count for MLL3, biological replicate 1, from the GEO per-oligo source table.
mll3_rep2_unique_tags
UMI-collapsed unique reporter-tag count for MLL3, biological replicate 2, from the GEO per-oligo source table.
mll3_rep3_unique_tags
UMI-collapsed unique reporter-tag count for MLL3, biological replicate 3, from the GEO per-oligo source table.
emsy_rep1_unique_tags
UMI-collapsed unique reporter-tag count for EMSY, biological replicate 1, from the GEO per-oligo source table.
emsy_rep2_unique_tags
UMI-collapsed unique reporter-tag count for EMSY, biological replicate 2, from the GEO per-oligo source table.
emsy_rep3_unique_tags
UMI-collapsed unique reporter-tag count for EMSY, 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.
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. 11,729 of 12,000 source rows retained and 271 excluded.
Curation notes
Source GEO accession: GSE126221. The focused human library includes promoter, enhancer, and random control sequences rather than only canonical promoters. No author-defined activated-CP table was provided for the HCT116 screen, 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.