Experiment / E52KB3NMSIntegrated lentiMPRA

Synthetic TFBS orientation and order lentiMPRA in HepG2

Transcription factor binding site orientation and order are major drivers of gene regulatory activity

Integrated lentiviral MPRA of 209,440 designed 200-bp sequences testing motif copy number, orientation, order, spacing, and combinations of 18 liver-associated or general transcription factor binding sites on two neutral backgrounds.

Download processed table (CSV)Raw source data API documentation

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: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Agilent oligo pool cloned into the pLS-SceI lentiMPRA vector; HepG2 cells infected at approximately MOI 50, with roughly 30 integrations per barcode; DNA and RNA barcodes were collected three days after infection in three independent replicates. The library includes one to eight homotypic motif copies, heterotypic pairs and triplets, all tested across orientation configurations where feasible.

Processed data

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

Visible columns (33 of 33)

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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 · 33 definitions

element_id: Source library identifier (seq_N; N is the 1-based library record index).
library_index: 1-based record index in Library_MPRA_TFBSs.txt.
sequence: 200-bp designed sequence after removing the invariant 15-bp flanking sequence from each end of the 230-bp oligo record.
library_header: Original design annotation from the source library header.
construct: Synthetic lentiMPRA background construct (Construct1 or Construct2).
background_context: Neutral background sequence context; Construct1 and Construct2 correspond to the two hg19 backgrounds described in the paper.
design_category: Parsed design class from the source header.
motif_names: Semicolon-separated ordered motif/TF names parsed from the design header; repeated names represent repeated copies when positions are available.
motif_count: Number of motif occurrences inferred from listed positions or motif names.
motif_orientation_pattern: Semicolon-separated motif orientations in construct order (template or non-template).
motif_positions: Semicolon-separated motif start positions within the designed sequence, as reported in the source header.
inter_motif_distances: Semicolon-separated inter-motif distances reported in the source header.
sequence_orientation: Overall sequence orientation when encoded for a non-synthetic reference/control record; blank for ordinary synthetic constructs.
rna_normalized_rep1: Source normalized RNA barcode abundance for independent replicate 1.
dna_normalized_rep1: Source normalized DNA barcode abundance for independent replicate 1.
rna_dna_ratio_rep1: Source RNA/DNA activity ratio for independent replicate 1.
log2_activity_rep1: Log2 of the source RNA/DNA activity ratio for independent replicate 1.
barcode_tags_rep1: Number of recovered barcode tags for independent replicate 1.
rna_normalized_rep2: Source normalized RNA barcode abundance for independent replicate 2.
dna_normalized_rep2: Source normalized DNA barcode abundance for independent replicate 2.
rna_dna_ratio_rep2: Source RNA/DNA activity ratio for independent replicate 2.
log2_activity_rep2: Log2 of the source RNA/DNA activity ratio for independent replicate 2.
barcode_tags_rep2: Number of recovered barcode tags for independent replicate 2.
rna_normalized_rep3: Source normalized RNA barcode abundance for independent replicate 3.
dna_normalized_rep3: Source normalized DNA barcode abundance for independent replicate 3.
rna_dna_ratio_rep3: Source RNA/DNA activity ratio for independent replicate 3.
log2_activity_rep3: Log2 of the source RNA/DNA activity ratio for independent replicate 3.
barcode_tags_rep3: Number of recovered barcode tags for independent replicate 3.
log2_activity_mean: Mean log2 activity across the three independent replicates.
log2_activity_sd: Sample standard deviation of log2 activity across the three independent replicates.
log2_activity_min: Minimum log2 activity across the three independent replicates.
log2_activity_max: Maximum log2 activity across the three independent replicates.
barcode_tags_min: Minimum barcode-tag count across the three independent replicates.

Quality control

The source analysis used MPRAflow-style UMI deduplication, BWA-MEM insert mapping with up to one mismatch, and removal of inserts with associated barcode counts below 3. For this package, only IDs present in all three independent replicate tables and with barcode tags >=3 in every replicate were retained (188548 of 209440 library records; intersection before barcode filtering: 192696). The processed table contains log2-transformed RNA/DNA ratios and replicate summaries.

Curation notes

The synthetic library is integrated lentiMPRA in HepG2 and contains 200-bp designs with invariant 15-bp oligo flanks in the raw 230-bp records. Construct1 and Construct2 are the two neutral genomic backgrounds described in the paper. The repository's normalized RNA and DNA columns and linear RNA/DNA ratio are retained per replicate; log2 activity columns are derived here. After QC, replicate Pearson correlations for log2 activity were 0.791, 0.737, and 0.763.

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