Experiment / E2QKY7RC2Targeted / Cap-STARR-seq

Human promoter CapStarr-seq activity in K562

Genome-wide characterization of mammalian promoters with distal enhancer functions

Approximately 250-bp human promoter windows centered on annotated transcription start sites, together with positive and negative controls, were tested by CapStarr-seq in K562 cells. The table reports RNA/input fold-change and replicate activity calls for the two biological replicates.

Download processed table (CSV)Raw source data API documentation

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:0004
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

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 GSM2198557 and GSM2198558, with GSM2198561 as the CapStarr input control.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (22 of 22)

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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: K562 replicate 1 RNA/input fold-change
fc_rep2: K562 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 K562 replicate fold-changes
sd_fc: Sample standard deviation of the two K562 replicate fold-changes
active_replicate_count: Number of K562 replicates whose source group label is Active
activity_class_rep1: Source K562 replicate 1 activity group
activity_class_rep2: Source K562 replicate 2 activity group
activity_definition: Source K562 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_K562 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 K562 replicate fold-change values were finite and positive, and both replicate activity labels were present. All 21,095 source rows passed these filters. No pseudocount or imputation was applied. Control rows were retained when they passed the same filters. Source condition-level Definition values represented by numeric 0 were treated as missing and emitted as blank.

Curation notes

K562 is represented by Cellosaurus CVCL:0004. 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 K562 score QC. No variants or rsIDs are assayed; the output is promoter regulatory activity.

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