Experiment / E3Y1K7E8HIntegrated lentiMPRA

Joint 60,000-element lentiMPRA library in WTC11

Massively parallel characterization of transcriptional regulatory elements

The same approximately 60,000-element joint library of potential enhancers, promoters, and controls was assayed in human WTC11 induced pluripotent stem cells in three independent lentiviral infections. The table includes the WTC11 activity score together with the cross-cell joint-library scores and element-specificity values reported by the study.

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:Y803
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The joint library used the same 230-nt oligo design (15-nt adaptors flanking a 200-bp element) and 15-nt random barcode strategy as the other libraries. It was delivered to WTC11 at an estimated MOI of 10 and harvested after three days; three independent infections were quantified by integrated DNA and RNA barcode sequencing with MPRAflow. The processed table preserves the source joint-library activity in all three cell types and the reported ESS cross-cell comparison fields.

Processed data

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Visible columns (49 of 49)

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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 · 49 definitions

element_id: Author-provided identifier for the designed cis-regulatory element or control construct.
element_category: Author-provided category such as potential enhancer, promoter, or control.
orientation: Reporter orientation inferred from the source identifier convention; forward/sense for unsuffixed names and reverse/antisense for reversed names.
chromosome: Primary chromosome coordinate, normalized with a chr prefix; GRCh38 is preferred and hg19 is used only when GRCh38 is unavailable.
start: Primary 0-based element start coordinate from the source design table.
end: Primary element end coordinate from the source design table.
strand: Primary source-design strand.
chr_hg38: Chromosome of the design mapped to GRCh38/hg38, normalized with a chr prefix.
start_hg38: Start coordinate of the design mapped to GRCh38/hg38.
end_hg38: End coordinate of the design mapped to GRCh38/hg38.
strand_hg38: Strand of the GRCh38/hg38 mapping.
chr_hg19: Chromosome of the convenience mapping to hg19/GRCh37, normalized with a chr prefix; blank when not supplied.
start_hg19: Start coordinate of the convenience mapping to hg19/GRCh37; blank when not supplied.
end_hg19: End coordinate of the convenience mapping to hg19/GRCh37; blank when not supplied.
strand_hg19: Strand of the hg19/GRCh37 mapping; blank when not supplied.
sequence_200bp: The 200-bp regulatory sequence tested in the reporter, extracted from the 230-nt oligo by removing the fixed 15-nt flanks.
activity_replicate_1: Published median-normalized log2(RNA/DNA) activity score for biological replicate 1 in this cell type.
activity_replicate_2: Published median-normalized log2(RNA/DNA) activity score for biological replicate 2 in this cell type.
activity_replicate_3: Published median-normalized log2(RNA/DNA) activity score for biological replicate 3 in this cell type.
activity_mean: Published mean activity score across the three biological replicates in this cell type.
normalized_dna_count_rep1: Published normalized integrated-DNA barcode count for replicate 1.
normalized_dna_count_rep2: Published normalized integrated-DNA barcode count for replicate 2.
normalized_dna_count_rep3: Published normalized integrated-DNA barcode count for replicate 3.
normalized_rna_count_rep1: Published normalized RNA barcode count for replicate 1.
normalized_rna_count_rep2: Published normalized RNA barcode count for replicate 2.
normalized_rna_count_rep3: Published normalized RNA barcode count for replicate 3.
rna_dna_ratio_rep1: Published normalized RNA/DNA ratio for replicate 1.
rna_dna_ratio_rep2: Published normalized RNA/DNA ratio for replicate 2.
rna_dna_ratio_rep3: Published normalized RNA/DNA ratio for replicate 3.
log2_activity_rep1: Full-precision replicate-level log2(RNA/DNA) score from the source replicate sheet for replicate 1.
log2_activity_rep2: Full-precision replicate-level log2(RNA/DNA) score from the source replicate sheet for replicate 2.
log2_activity_rep3: Full-precision replicate-level log2(RNA/DNA) score from the source replicate sheet for replicate 3.
observed_barcodes_rep1: Number of independent element-associated barcodes observed in replicate 1.
observed_barcodes_rep2: Number of independent element-associated barcodes observed in replicate 2.
observed_barcodes_rep3: Number of independent element-associated barcodes observed in replicate 3.
mean_normalized_dna_count: Mean normalized DNA barcode count across the three replicates.
mean_normalized_rna_count: Mean normalized RNA barcode count across the three replicates.
mean_observed_barcodes: Mean observed barcode count across the three replicates.
min_observed_barcodes: Minimum observed barcode count among the three replicates.
total_observed_barcodes: Sum of observed barcode counts across the three replicates.
activity_hepg2_joint: Mean median-normalized log2(RNA/DNA) activity for the element in HepG2 from the joint-library summary.
activity_k562_joint: Mean median-normalized log2(RNA/DNA) activity for the element in K562 from the joint-library summary.
activity_wtc11_joint: Mean median-normalized log2(RNA/DNA) activity for the element in WTC11 from the joint-library summary.
joint_element_type: Element category/type recorded in the joint-library element-specificity summary.
ess_hepg2: HepG2 element-specificity score reported for the joint library, comparing HepG2 activity with the element's cross-cell mean.
ess_k562: K562 element-specificity score reported for the joint library, comparing K562 activity with the element's cross-cell mean.
ess_wtc11: WTC11 element-specificity score reported for the joint library, comparing WTC11 activity with the element's cross-cell mean.
source_activity_table: Supplementary joint-library activity workbook and cell-type sheet used to obtain the activity values.
qc_pass: Boolean package-QC flag; true for every retained row in this table.

Quality control

The authors removed elements measured with fewer than 10 independent barcodes, median-normalized activity within each replicate, and averaged three independent infections. Package QC retained 55,870 WTC11 rows from the published joint-library summary after requiring finite activity values, a matching valid 200-bp design sequence, three replicate-level barcode/count records, and at least 10 observed barcodes in each replicate; non-element or non-finite records were excluded.

Curation notes

This is the WTC11 view of the shared joint library; the activity_hepg2_joint/activity_k562_joint/activity_wtc11_joint and ESS columns are copied from the same joint summary for cross-cell comparison. The source design contains hg19 and hg38 coordinates for many elements; GRCh38 is primary. Coordinate-bearing control names were joined after deterministic normalization of source bracket notation where necessary. The package contains 55,870 finite, sequence-linked WTC11 summary records after the stated ten-barcode-per-replicate QC filter; raw sequencing reads were intentionally omitted.

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