A lentiviral MPRA library tested 74 overlapping tiles spanning an approximately 860 bp candidate enhancer interval in the first intron of human LDLR, together with three positive and three negative control sequences. HuH7 cells received five independent library transductions, and reporter activity was measured two days later as barcode cDNA abundance relative to genomic DNA.
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:0336
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
chr19:11090150-11091008
Perturbation & assay details
Basal / Untreated
The library was assembled in the pLS-SceI reporter backbone with a random 15 bp 5' UTR barcode, packaged as lentivirus, and transduced at an estimated MOI of 5. The library contained overlapping 172, 129, 86, and 43 bp tiles plus three positive and three negative controls; HuH7 cells were harvested two days after transduction for genomic DNA and RNA. Barcode counts were normalized to counts per million, aggregated by construct, and summarized as the mean cDNA/gDNA ratio for five independent transductions, normalized to the average negative-control activity.
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 · 18 definitions
element_id
Construct identifier from the authors' MPRA library (Tile-#, Pos-#, or Neg-#).
element_type
Construct class: candidate_tile, positive_control, or negative_control.
chrom
Chromosome for candidate tiles in GRCh38; blank for control sequences.
start_hg38
Inclusive hg38 start coordinate reported in the MPRA library design; blank for controls.
end_hg38
Inclusive hg38 end coordinate reported in the MPRA library design; blank for controls.
sequence
Test or control DNA sequence used in the MPRA library.
sequence_length
Length of the test or control sequence in base pairs.
variant_context
Variant annotation reported for the construct (rs59281581 where present, none otherwise, or control_sequence for controls).
barcode_count
Number of retained barcode-to-construct associations in S7 Table.
barcode_mapping_read_count
Sum of Read Count across retained barcode-to-construct associations for the construct.
activity_ratio
Normalized aggregate cDNA/gDNA activity ratio for HuH7, normalized to the mean negative-control activity.
log2_activity_ratio
Base-2 logarithm of activity_ratio, calculated from the packaged table.
activity_rep1_ratio
HuH7 normalized cDNA/gDNA activity ratio for independent replicate 1.
activity_rep2_ratio
HuH7 normalized cDNA/gDNA activity ratio for independent replicate 2.
activity_rep3_ratio
HuH7 normalized cDNA/gDNA activity ratio for independent replicate 3.
activity_rep4_ratio
HuH7 normalized cDNA/gDNA activity ratio for independent replicate 4.
activity_rep5_ratio
HuH7 normalized cDNA/gDNA activity ratio for independent replicate 5.
qc_status
pass; construct is present in the authors' post-QC expression analysis with complete replicate measurements.
Quality control
The authors filtered barcode-to-construct associations to retain combinations with at least 10 reads and barcodes with at least 99% of reads assigned to one construct; expression barcodes with fewer than 10 counts across all samples were removed. The processed table retains the 69 detected candidate tiles plus three positive and three negative controls present in S9 Table, with complete five-replicate values. Expected Tile-4, Tile-5, Tile-22, Tile-23, and Tile-41 were absent from the plasmid pool and are excluded.
Curation notes
This is the HuH7 arm of the same integrated lentiMPRA library also tested in HepG2. The test sequences are region-focused and use the population-major allele design reported by the authors, including the common insertion rs59281581 that is absent from the hg38 reference; this is not an allele-contrast MPRA. Controls are retained to make the authors' negative-control normalization and positive-control behavior directly inspectable.