Experiment / E4U6C4U1QIntegrated lentiMPRA

Large-scale WTC11 lentiMPRA library

Massively parallel characterization of transcriptional regulatory elements

A 75,542-element library comprising promoters, a sampled set of potential enhancers, and controls was assayed in human WTC11 induced pluripotent stem cells in three independent lentiviral infections. Element activity was quantified from integrated DNA and RNA barcodes as normalized log2(RNA/DNA) scores.

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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

Agilent oligonucleotides were 230 nt, consisting of a fixed 15-nt 5′ adaptor, a 200-bp test element, and a fixed 15-nt 3′ adaptor. A 15-nt random barcode was added during amplification before cloning into the pLS-SceI reporter vector; the lentiviral library was packaged in HEK293T cells, delivered to WTC11 at an estimated MOI of 10, and harvested after three days. Three independent infections were sequenced for integrated DNA and RNA barcodes with MPRAflow, and activity was reported as median-normalized log2(RNA/DNA).

Processed data

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

Visible columns (42 of 42)

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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 · 42 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 by the source design table.
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.
activity_replicate_2: Published median-normalized log2(RNA/DNA) activity score for biological replicate 2.
activity_replicate_3: Published median-normalized log2(RNA/DNA) activity score for biological replicate 3.
activity_mean: Published mean activity score across the three biological replicates.
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.
source_activity_table: Supplementary 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 47,252 rows from the published summary activity records 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

WTC11 is the GM25256 human iPSC line (Cellosaurus CVCL:Y803). The source design workbook is represented on GRCh38; hg19 convenience fields are blank where not supplied. The authors used the lower MOI of 10 because higher infection levels were lethal to WTC11. The raw_data archive preserves the complete final supplementary-table ZIP, while raw sequencing reads were intentionally omitted. The package contains 47,252 finite, sequence-linked summary records.

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