The shared 59,470-barcode library represented motif-focused and 160-bp tiled LTR18A fragments, ancestral reconstructions, reverse complements, motif mutants, and controls; it was transfected into human HepG2 liver carcinoma cells. Three biological transfections were measured by RNA/DNA barcode enrichment normalized to the basal hsp68 promoter.
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
Agilent-synthesized approximately 230-bp oligos carried 160-bp or shorter LTR18A-derived inserts upstream of an hsp68 minimal promoter driving dsRed in a pGL4-derived episomal plasmid; each synthesized library element was assigned 10 unique barcodes, with 300 barcodes for the basal-promoter control. Five micrograms of library was electroporated into 1.2 million cells per replicate; RNA was collected 24 hours after transfection. Element-level counts were normalized to counts per million, RNA CPM/DNA CPM was normalized to the average basal-construct expression, and enrichment was reported as log2 normalized expression.
Processed data
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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 · 19 definitions
element_id
Original element identifier from the HepG2 enrichment-score release, including LTR18A fragments, ancestral reconstructions, tiles, controls, motif mutants, and full-element aggregates.
sequence
Synthesized insert sequence from MPRA_library_design.tsv; empty for the basal-promoter placeholder and for published full-element aggregates without a supplied design sequence.
sequence_length_bp
Length in base pairs of the available synthesized insert sequence; empty when sequence is unavailable.
sequence_available
Boolean indicating whether a synthesized insert sequence was available in the library-design source.
library_component
Package classification of the library element: motif_focused, tiled_fragment, motif_mutagenesis, reverse_complement, external_control_ernst2016, negative_control_shuffled, basal_control, or full_element_aggregate.
source_species_or_state
Species token or inferred evolutionary/control state preserved or parsed from the element identifier.
source_locus
Broad chromosome interval parsed from the element identifier when present; coordinates follow the source hg19 naming and are not independently remapped.
orientation
Whether the identifier marks a reverse-complement construct or a forward/unspecified construct.
tile_index
Zero-based tile number parsed from identifiers containing |tile_N; empty for non-tiled elements.
barcode_count
Number of barcode records associated with the element in MPRA_library_design.tsv, or in the corresponding GEO barcode-count file for a full-element aggregate.
replicate_1_enrichment_score
Published HepG2 replicate-1 enrichment score, defined as log2 RNA/DNA expression normalized to the basal hsp68-promoter construct.
replicate_2_enrichment_score
Published HepG2 replicate-2 enrichment score on the same log2 normalized RNA/DNA scale.
replicate_3_enrichment_score
Published HepG2 replicate-3 enrichment score on the same log2 normalized RNA/DNA scale.
enrichment_score_mean
Arithmetic mean of the three published HepG2 replicate enrichment scores, derived by this package.
enrichment_score_sd
Sample standard deviation of the three published HepG2 replicate enrichment scores, derived by this package.
enrichment_score_median
Median of the three published HepG2 replicate enrichment scores, derived by this package.
active_enrichment_gt_1
Boolean indicating whether the mean enrichment score exceeds 1, the paper's active-element threshold corresponding to more than twofold activity over basal.
replicate_count
Number of published HepG2 transfection replicate scores represented in the row.
score_source
Filename of the processed GEO/Supplemental Data S1 score source used for this experiment.
Quality control
The authors summed barcode counts per element and filtered elements with fewer than 5 total counts in any of the three transfection replicates or plasmid-DNA input. Published scores were highly reproducible in HepG2 (mean replicate R2 = 0.904). Package QC retained all 5,937 unique HepG2 score rows because all three published replicate scores were finite and every row had a matching GEO barcode-count record; sequences and barcode multiplicities were joined from MPRA_library_design.tsv when available. No source-score row was removed; 19 published full-element aggregate rows lack a sequence in the design file and are retained with sequence_available=false.
Curation notes
HepG2 is resolved to Cellosaurus CVCL:0027. This is a region-focused TE-subfamily screen rather than an allele-pair variant assay; the library contains natural sequence diversity and targeted JUN/DBP motif mutants. Four HepG2 RNA barcode-count files and three plasmid-DNA input files are preserved in raw_data as GEO provenance, while the processed table uses the authors' published three-replicate enrichment columns. The source score release contains 5,918 synthesized elements plus 19 full-element aggregate outputs; the latter have barcode counts but no corresponding sequence row in the supplied library design.