Human promoter CapStarr-seq activity in HeLa-S3
Genome-wide characterization of mammalian promoters with distal enhancer functionsApproximately 250-bp human promoter windows centered on annotated transcription start sites, together with positive and negative controls, were tested by CapStarr-seq in HeLa/HeLa-S3 cells. The table reports RNA/input fold-change and replicate activity calls for the two biological replicates.
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
Basal / Untreated
Capture-enriched STARR-seq in an episomal mammalian reporter vector. The library covers −200 to +50 bp around the TSS of 20,719 human protein-coding genes plus four positive controls and 370 random negative/control regions. Reporter RNA signal was normalized to plasmid/input signal; biological replicates are GSM2198559 and GSM2198560, with GSM2198561 as the CapStarr input control.
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 · 22 definitions
- element_id
- Assayed promoter or control interval in source chr:start-end form
- category
- Source library category: promoter, Positive, or Negative
- chromosome
- Human chromosome parsed from element_id
- start_hg19
- Interval start coordinate parsed from the source hg19 coordinate
- end_hg19
- Interval end coordinate parsed from the source hg19 coordinate
- element_length_bp
- End minus start in base pairs
- strand
- Source strand for the promoter/control sequence
- gene_id
- Source associated gene identifier, blank for controls
- transcript_id
- Source associated transcript identifier, blank for controls
- fc_rep1
- HeLa replicate 1 RNA/input fold-change
- fc_rep2
- HeLa replicate 2 RNA/input fold-change
- log2_fc_rep1
- Base-2 logarithm of fc_rep1
- log2_fc_rep2
- Base-2 logarithm of fc_rep2
- mean_fc
- Arithmetic mean of the two HeLa replicate fold-changes
- sd_fc
- Sample standard deviation of the two HeLa replicate fold-changes
- active_replicate_count
- Number of HeLa replicates whose source group label is Active
- activity_class_rep1
- Source HeLa replicate 1 activity group
- activity_class_rep2
- Source HeLa replicate 2 activity group
- activity_definition
- Source HeLa condition-level definition: Active or Inactive; blank for source numeric 0/unclassified
- source_promoter_type
- Source Promoter type field, usually Non-Epromoter when populated
- promoter_activity_profile
- Derived condition label: Epromoter_HeLa for promoter rows with Active definition, Non-Epromoter for matching inactive source labels, control for Positive/Negative rows, otherwise an explicit unclassified/not-active label
- qc_pass
- TRUE for rows passing the package QC filters
Quality control
Rows were retained when the source coordinate matched chr:start-end with end greater than start, category was promoter, Positive, or Negative, both HeLa replicate fold-change values were finite and positive, and both replicate activity labels were present. This retained 21,075 of 21,095 source rows and excluded 20 promoter rows with non-positive HeLa fold-change. No pseudocount or imputation was applied. Control rows were retained when they passed these filters. Source condition-level Definition values represented by numeric 0 were treated as missing and emitted as blank.
Curation notes
The GEO series labels these samples HeLa, while the study and related descriptions refer to HeLa-S3; Cellosaurus CVCL:0058 is used for the HeLa-S3 line. The table is generated from the higher-precision Supplementary Table 2a rather than the rounded GEO text export. All 370 Negative and 6 Positive control rows passed the HeLa score QC. No variants or rsIDs are assayed; the output is promoter regulatory activity.