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Experiment / E6PW8MKAJEpisomal Plasmid MPRA

Episomal pGL4.23c MPRA of HepG2 candidate liver enhancers

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

The common 2,440-element library was cloned with 171-bp candidate liver enhancers upstream of the pGL4.23c minimal promoter and reporter, with linked barcodes in the reporter 3' UTR. Plasmid libraries were transfected into HepG2 cells in three independent replicate cultures.

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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

Classic pGL4.23c enhancer MPRA: 171-bp enhancer/control sequence upstream of a minimal promoter, a 15-bp degenerate barcode in the reporter 3' UTR, transient plasmid transfection, and matched DNA/RNA barcode sequencing.

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 · 20 definitions
element_id
Published identifier for the tested 171-bp enhancer or control element.
element_type
Source element class: test, pos control, or neg control.
chromosome
Human hg19 chromosome for the source element; blank for synthetic controls without a genomic coordinate.
start
1-based hg19 start coordinate of the 171-bp source element; blank when unavailable.
end
1-based hg19 end coordinate of the 171-bp source element; blank when unavailable.
sequence
The 171-bp DNA sequence tested in the assay.
sequence_length_bp
Length of sequence in base pairs.
activity_mean_log2_rna_dna
Authors' activity score: mean log2 RNA/DNA after per-replicate median normalization; the source excludes the low-quality replicate 1 for 5'/3' MT and 3'/3' MT.
replicate_1_normalized_rna_cpm
Normalized RNA barcode count for replicate 1, reported as counts per million in the authors' pipeline.
replicate_1_normalized_dna_cpm
Normalized DNA barcode count for replicate 1, reported as counts per million in the authors' pipeline.
replicate_1_log2_rna_dna_ratio
Raw per-replicate log2(RNA/DNA) activity value for replicate 1, before the across-replicate median normalization used for the published mean.
replicate_1_unique_barcodes
Number of unique barcodes assigned to the element in replicate 1.
replicate_2_normalized_rna_cpm
Normalized RNA barcode count for replicate 2, reported as counts per million in the authors' pipeline.
replicate_2_normalized_dna_cpm
Normalized DNA barcode count for replicate 2, reported as counts per million in the authors' pipeline.
replicate_2_log2_rna_dna_ratio
Raw per-replicate log2(RNA/DNA) activity value for replicate 2, before the across-replicate median normalization used for the published mean.
replicate_2_unique_barcodes
Number of unique barcodes assigned to the element in replicate 2.
replicate_3_normalized_rna_cpm
Normalized RNA barcode count for replicate 3, reported as counts per million in the authors' pipeline.
replicate_3_normalized_dna_cpm
Normalized DNA barcode count for replicate 3, reported as counts per million in the authors' pipeline.
replicate_3_log2_rna_dna_ratio
Raw per-replicate log2(RNA/DNA) activity value for replicate 3, before the across-replicate median normalization used for the published mean.
replicate_3_unique_barcodes
Number of unique barcodes assigned to the element in replicate 3.

Quality control

Author QC was retained: barcode-to-element associations required at least three independent observations and at least 90% of barcode sequence mapped to one element; only barcodes observed in both the DNA and RNA sample were counted; UMI-collapsed counts were normalized to counts per million; and replicate RNA/DNA ratios were median-normalized before averaging. Package QC retained only rows with a valid A/C/G/T 171-bp sequence, finite published mean and replicate activity values, and finite source RNA, DNA, and unique-barcode fields for all three replicates. 2424 rows passed from 2429 source mean-score rows; 5 incomplete/missing rows were excluded. No extra minimum-barcode cutoff was imposed because the paper uses its measured element set for assay comparisons; observed barcode counts remain in the table.

Curation notes

The pGL4 assay-specific source sheet contains the count/activity fields used here. The table retains 2424 complete elements from the 2429 rows in the authors' all-assay mean table; 5 rows with missing or incomplete assay-specific source fields were omitted because the normalized count/activity record could not be represented completely.

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