Experiment / E2ZI2RCJ9Episomal Plasmid MPRA

pGL4 MPRA sequence-length comparison (192 bp, 354 bp, and 678 bp)

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

The same candidate liver-enhancer library was assembled as short (192-bp), medium (354-bp), and long (678-bp) genomic-context sequences, cloned into pGL4.23c, pooled, and transfected into HepG2 cells. Four independent replicate cultures were profiled by matched DNA and RNA barcode sequencing.

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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

The pGL4.23c reporter contained the enhancer sequence upstream of a minimal promoter and reporter, with a 15-bp molecular barcode in the reporter 3' UTR. Short elements were 192 bp, medium elements 354 bp, and long elements 678 bp; the deposited table contains one row per element-size combination.

Processed data

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

Visible columns (26 of 26)

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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 · 26 definitions

element_id: Published element identifier including the size suffix (_short, _medium, or _long).
parent_element_id: Element identifier without the size suffix, used to match the same candidate across lengths.
element_type: Source element class: test, pos control, or neg control.
size_class: Tested sequence size class: short (192 bp), medium (354 bp), or long (678 bp).
chromosome: Human hg19 chromosome; blank for synthetic controls without a genomic coordinate.
start: 1-based hg19 start coordinate of the element; blank when unavailable.
end: 1-based hg19 end coordinate of the element; blank when unavailable.
sequence: DNA sequence tested for the indicated size class.
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; package QC requires at least 10.
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; package QC requires at least 10.
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; package QC requires at least 10.
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; package QC requires at least 10.

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 length analysis required at least 10 unique barcodes per element. Package QC applied that threshold to all four replicate barcode counts, required finite source RNA, DNA, RNA/DNA ratio, and activity fields, and required a valid A/C/G/T sequence of the expected length. 5106 rows passed from 6020 source rows; 914 rows were excluded. 661 parent elements have all three size classes after QC.

Curation notes

The table is long-format: one row per retained element-size combination. The source contains fewer long constructs than short/medium constructs because not every long assembly was recovered with sufficient barcode support. The three-size subset includes candidate elements and any controls that met the same per-replicate >=10-barcode rule.

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