K562 silencer activity screen of human uncharacterized CREs

A plasmid STARR-seq-style silencer MPRA tested 7,440 human uncharacterized cis-regulatory elements alongside known enhancer, known silencer, and random-region controls in K562 cells. The library used 200-nt genomic inserts downstream of the SCP1 super core promoter and was measured in five biological RNA/DNA replicate pairs.

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

Episomal plasmid reporter using a human STARR-seq configuration with the SCP1 super core promoter; each genomic insert is transcribed and serves as its own sequence barcode. RNA and plasmid/DNA libraries were sequenced on an Illumina NextSeq 500 (1 x 75 cycles), and activity was evaluated from RNA/DNA ratios normalized to random-region controls.

Quality control

The authors checked RNA and plasmid reads with FASTQC, removed adapters and reads below Q20 with TrimGalore, mapped trimmed reads to hg19 with Bowtie2, and quantified tested sequences with featureCounts. Biological replicates were checked for similarity; sequences were retained only when detected in at least three of five biological replicates in both RNA and plasmid libraries. For the packaged table, detection was operationalized as a count greater than zero in at least three RNA replicates and at least three DNA replicates, retaining 7,317 of 7,547 GEO elements and excluding 230 low-coverage elements. Author-provided one-tailed t-test P values and Benjamini-Hochberg adjusted P values are retained for tested elements.

Curation notes

This is one MPRA experiment; the paper describes it as a STARR-seq approach for silencer testing, so it is classified here as Silencer / Repressor MPRA. The prose reports approximately 7,430 tested uncharacterized CREs, while both the GEO matrix and Supplementary Data 2 contain 7,440 tested rows. The processed table follows the deposited files and contains 7,232 QC-passing tested CREs, of which 3,001 are labeled MPRA_validated_silencer=YES, plus 85 QC-passing controls. The 45 retained random controls are included with raw counts but have blank author activity statistics because they form the normalization reference. No allele-specific variants or sequence reads were included; this region-focused screen reports genomic intervals and regulatory activity rather than variant effects.

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K562 silencer activity screen of human uncharacterized CREs

Processed data

Quality control

Curation notes

Cite OpenMPRA

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