Experiment / E299YPMR1Episomal Plasmid MPRA

pGL4 MPRA enhancer orientation comparison (forward versus reverse)

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

A 2,336-element 192-bp enhancer/control library was directionally cloned in both orientations upstream of the pGL4.23c minimal promoter and transfected into HepG2 cells. Four independent replicate cultures were profiled by matched DNA and RNA barcode sequencing.

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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

The 192-bp candidate sequence was placed upstream of the pGL4.23c minimal promoter and reporter, with associated barcodes in the reporter 3' UTR. Forward and Reverse rows share the source element and differ by the orientation of the tested sequence; Reverse sequences are reverse complements derived from the deposited forward sequence.

Processed data

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

Visible columns (27 of 27)

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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 · 27 definitions

element_id: Published element identifier including the tested orientation suffix (_F or _R).
parent_element_id: Published element identifier without the orientation suffix.
element_type: Source element class: test, pos control, or neg control.
orientation: Forward or Reverse orientation relative to the source reference sequence.
chromosome: Human hg19 chromosome; blank for synthetic controls without a genomic coordinate.
start: 1-based hg19 start coordinate of the source element; blank when unavailable.
end: 1-based hg19 end coordinate of the source element; blank when unavailable.
reference_sequence_192bp: 192-bp source sequence in the reference/forward orientation.
tested_sequence_192bp: Sequence used in the reporter construct: reference sequence for Forward and its reverse complement for Reverse.
sequence_length_bp: Length of sequence in base pairs.
activity_mean_log2_rna_dna: Authors' mean log2 RNA/DNA activity score after per-replicate median normalization.
replicate_1_normalized_rna: Normalized RNA barcode abundance for replicate 1 from the source table.
replicate_1_normalized_dna: Normalized DNA barcode abundance for replicate 1 from the source table.
replicate_1_rna_dna_ratio: Source RNA/DNA ratio for replicate 1 before the published median normalization.
replicate_1_unique_barcodes: Number of unique barcodes per element in replicate 1.
replicate_2_normalized_rna: Normalized RNA barcode abundance for replicate 2 from the source table.
replicate_2_normalized_dna: Normalized DNA barcode abundance for replicate 2 from the source table.
replicate_2_rna_dna_ratio: Source RNA/DNA ratio for replicate 2 before the published median normalization.
replicate_2_unique_barcodes: Number of unique barcodes per element in replicate 2.
replicate_3_normalized_rna: Normalized RNA barcode abundance for replicate 3 from the source table.
replicate_3_normalized_dna: Normalized DNA barcode abundance for replicate 3 from the source table.
replicate_3_rna_dna_ratio: Source RNA/DNA ratio for replicate 3 before the published median normalization.
replicate_3_unique_barcodes: Number of unique barcodes per element in replicate 3.
replicate_4_normalized_rna: Normalized RNA barcode abundance for replicate 4 from the source table.
replicate_4_normalized_dna: Normalized DNA barcode abundance for replicate 4 from the source table.
replicate_4_rna_dna_ratio: Source RNA/DNA ratio for replicate 4 before the published median normalization.
replicate_4_unique_barcodes: Number of unique barcodes per element in replicate 4.

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 DNA and RNA were counted; normalized counts and median-normalized activity scores were used; and the paper reports median barcode counts above 100 and Pearson reproducibility above 0.98. Package QC required a valid A/C/G/T 192-bp sequence and finite activity, RNA, DNA, RNA/DNA ratio, and unique-barcode values for all four replicates. No additional minimum-barcode cutoff was imposed. 4547 rows passed from 4549 source orientation rows; 2 incomplete rows were excluded.

Curation notes

One row is emitted for each retained element-orientation combination. The source has 2,336 designed elements but not every orientation has a complete deposited activity record; incomplete source rows were omitted. Forward/Reverse sequence orientation for the Reverse rows is derived as the reverse complement of the deposited reference sequence.

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