Experiment / E79SJQHVRTargeted / Cap-STARR-seq

K562 promoter CapSTARR-seq: untreated versus IFNα stimulation

Epromoters function as a hub to recruit key transcription factors required for the inflammatory response

A capture-based promoter CapSTARR-seq library was tested in human K562 cells in untreated and IFNα-stimulated conditions. The table contains promoter-level enhancer activity, replicate measurements, author-defined Epromoter calls, and matched RNA-seq expression context for the 17,941 retained promoter elements.

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 versus 50 ng/mL IFNα (interferon alpha 2a) for 6 h

The capture library targeted -200 to +50 bp relative to the TSS of human protein-coding genes and included random genomic controls in the original design. The study transfected 50 million K562 cells with 1.25 mg of library, treated cells 18 h later with 50 ng/mL IFNα for 6 h in duplicate, and sequenced poly(A) reporter RNA and input-library material on an Illumina NextSeq 500. Reads were trimmed at Q20, mapped to hg19 with Bowtie2, and quantified as CapSTARR-seq signal divided by the input library; the supplied table reports the authors' two replicate signals and normalized activity values for untreated and IFNα conditions.

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 · 34 definitions

element_id: Unique generated identifier for the tested promoter record in the form chr:start-end:strand:gene; the gene suffix distinguishes alternative RefSeq-associated records sharing identical coordinates.
chr_hg19: Chromosome of the promoter window in the hg19 reference assembly.
start_hg19: Reported start coordinate of the promoter capture window in hg19.
end_hg19: Reported end coordinate of the promoter capture window in hg19.
strand: RefSeq TSS strand reported for the promoter.
gene: RefSeq-associated gene name for the promoter element.
library_element_type: Source library element category; hPro denotes a human promoter.
input_signal: CapSTARR-seq input-library signal reported by the authors.
untreated_signal_rep1: CapSTARR-seq reporter signal for untreated K562 replicate 1.
untreated_activity_rep1: Untreated replicate 1 reporter signal divided by input-library signal.
untreated_active_rep1: Author inflection-point activity call for untreated replicate 1.
untreated_signal_rep2: CapSTARR-seq reporter signal for untreated K562 replicate 2.
untreated_activity_rep2: Untreated replicate 2 reporter signal divided by input-library signal.
untreated_active_rep2: Author inflection-point activity call for untreated replicate 2.
untreated_activity_mean: Arithmetic mean of the two untreated normalized reporter activity values.
ifna_signal_rep1: CapSTARR-seq reporter signal for IFNα-stimulated K562 replicate 1.
ifna_activity_rep1: IFNα replicate 1 reporter signal divided by input-library signal.
ifna_active_rep1: Author inflection-point activity call for IFNα replicate 1.
ifna_signal_rep2: CapSTARR-seq reporter signal for IFNα-stimulated K562 replicate 2.
ifna_activity_rep2: IFNα replicate 2 reporter signal divided by input-library signal.
ifna_active_rep2: Author inflection-point activity call for IFNα replicate 2.
ifna_activity_mean: Arithmetic mean of the two IFNα normalized reporter activity values.
ifna_vs_untreated_fold_change: Authors' IFNα-versus-untreated fold change, equal to mean IFNα activity divided by mean untreated activity.
ifna_vs_untreated_log2_fold_change: Base-2 logarithm of the IFNα-versus-untreated activity fold change, calculated during packaging.
epromoter_type: Author-defined promoter class: induced, constitutive, or repressed Epromoter; blank means no Epromoter class was assigned.
gene_expression_class: Author RNA-seq gene-expression response class: Induced, Repressed, or blank when not significant/applicable.
rna_untreated_rep1: RNA-seq expression value for untreated K562 replicate 1, as supplied by the authors.
rna_untreated_rep2: RNA-seq expression value for untreated K562 replicate 2, as supplied by the authors.
rna_untreated_rep3: RNA-seq expression value for untreated K562 replicate 3, as supplied by the authors.
rna_ifna_rep1: RNA-seq expression value for IFNα-stimulated K562 replicate 1, as supplied by the authors.
rna_ifna_rep2: RNA-seq expression value for IFNα-stimulated K562 replicate 2, as supplied by the authors.
rna_ifna_rep3: RNA-seq expression value for IFNα-stimulated K562 replicate 3, as supplied by the authors.
gene_expression_log2_fold_change: DESeq2 log2 fold change for gene expression under IFNα versus untreated conditions.
gene_expression_padj: DESeq2 adjusted P-value for the IFNα-versus-untreated gene-expression contrast.

Quality control

The authors removed 421 promoter regions with input-library FPKM <1, leaving 17,941 promoter elements, and reported Pearson R² >0.9 between CapSTARR-seq replicates. They called Epromoters above the ranked-signal inflection point and defined IFNα-induced Epromoters by an average IFNα/untreated activity ratio >2 with at least one active replicate. For packaging, rows were additionally required to have valid hg19 chromosome coordinates, strand and gene labels, a positive input signal, and finite values for all ten primary MPRA signal/activity fields. All 17,941 source rows passed these checks; no valid measured promoter was removed for being inactive or lacking an Epromoter call. Source NA annotations are represented as empty CSV fields.

Curation notes

This is one MPRA experiment with two biological conditions, not separate experiments: promoter activity was measured in untreated and IFNα-stimulated K562 cells. Supplementary Dataset 1 is the authors' promoter-level summary rather than barcode-level counts or sequences; the processed table retains all 17,941 measured promoter rows after the authors' input filter. GEO lists four CapSTARR-related records (replicate 1/2 and corresponding Seq2 records), while the supplied summary reports two assay replicates per condition. The library is region-focused and not allele-specific; no rsIDs or variant contrasts were reported. The table includes RNA-seq columns only as matched biological context, with CapSTARR-seq activity columns as the primary assay output.

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