ENCODE HepG2 candidate regulatory-element lentiMPRA

Secondary analysis of an ENCODE integrated lentiMPRA library containing 164,307 HepG2 candidate regulatory-element sequences; the public processed quantification provides meanVal activity for a subset and includes forward/reverse construct pairs used to study motif orientation and order.

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:0027
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

ENCODE-provided processed element quantification (meanVal) joined to the 200-bp reference FASTA. The paper used FIMO motif calls on this library to test TFBS orientation, order, and position effects; this package retains the measured element activity, sequence, source labels, and paired orientation difference without re-running motif calling.

Quality control

The public ENCODE quantification file is a processed element-level output without barcode-count columns. Rows were retained when the element name exactly matched the reference FASTA or had a unique canonical base/orientation alias, the sequence was a finite 200-bp A/C/G/T/N sequence, and meanVal was finite (138182 of 138182 quantified rows; 164307 reference sequences were available; 7 quantification rows used a unique orientation alias). No additional activity cutoff was applied.

Curation notes

This is the secondary ENCODE HepG2 lentiMPRA analyzed by the paper, not the paper's synthetic library. The downloaded reference FASTA file is annotated by ENCODE as hg19, while the ENCSR359FTN reference record is tagged GRCh38 and individual source identifiers include hg18, hg19, and mm9 labels; the table preserves these source assembly labels. Many candidate elements lack explicit coordinates. Forward/reverse orientation pairs are annotated for 59878 complete pairs (119756 rows).

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ENCODE HepG2 candidate regulatory-element lentiMPRA

Processed data

Quality control

Curation notes

Cite OpenMPRA

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