A lentivirus-integrated MPRA tested 171-bp human and chimpanzee orthologous sequences from 714 HARs together with positive and negative controls. The library was measured in human WTC and HS1-11 and chimpanzee Pt2A iPSC-derived neural cells at N2 and N3 stages; the deposited Pt5C runs are retained in raw_data but excluded from this QC-passed table.
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
Not reported
Taxonomy ID
Not reported / not applicable
Biosample
Not reported / not applicable
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Array-synthesized 171-bp candidate sequences carried universal priming sites, a spacer, and a designed 15-bp barcode and were cloned into the pLS-mP lentiviral reporter. Cells were infected at an MOI of approximately 50; poly(A) RNA and genomic DNA barcode libraries were sequenced with paired 15-bp barcode reads and 10-bp UMIs. RNA/DNA activity is reported after replicate-level CPM normalization and aggregation across barcodes and tiled oligos.
Processed data
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Visible columns (29 of 29)
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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 · 29 definitions
element_id
Stable package identifier; HAR alleles are named HAR|species and controls retain their GEO construct annotation.
element_name
HAR name, permutation parent, or control annotation without the sequence-species suffix.
element_class
HAR, Positive control, Negative control, or Control.
sequence_species
Species of the tested HAR allele (human or chimp); blank for controls.
parent_har
Parent HAR name for an allele; blank for controls.
permutation_index
Not applicable for the main library; null/blank for non-permutation elements.
permutation_total
Not applicable for the main library; null/blank for non-permutation elements.
variant_description
Not applicable for the main library; null/blank for non-permutation elements.
coordinates_hg19
Tested hg19 coordinate(s) encoded in the original construct annotation; semicolon-separated for tiled HARs.
oligo_count
Number of distinct construct annotations/tiles aggregated into this element.
representative_annotation
One original GEO construct annotation without the final barcode ordinal.
rna_sample_accession
GEO sample accession for the RNA barcode-count file.
dna_sample_accession
GEO sample accession for the matched DNA barcode-count file.
Organism of the iPSC-derived cellular environment: human or chimpanzee.
cell_line
iPSC line used for the cellular trans environment.
differentiation_stage
N2 neural progenitor or N3 glial progenitor stage.
technical_replicate
Technical replicate number from the GEO sample label.
library_type
Main HAR ortholog library.
rna_count
Sum of RNA barcode counts for barcodes detected in the matched DNA file.
dna_count
Sum of DNA barcode counts for the element.
rna_cpm
RNA count normalized to total RNA counts in that replicate and scaled to one million.
dna_cpm
DNA count normalized to total DNA counts in that replicate and scaled to one million.
dna_barcode_count
Number of unique detected DNA barcodes contributing to the element.
rna_barcode_count_on_dna
Number of matched DNA-detected barcodes also observed in RNA.
log2_rna_dna
Log2 of the CPM-normalized RNA/DNA activity ratio for this element and replicate.
condition_mean_log2_rna_dna
Mean log2 RNA/DNA activity across the three replicates for the cell-species/cell-line/stage condition.
cis_delta_human_minus_chimp
For paired HAR alleles, condition mean activity of the human sequence minus the chimpanzee sequence in the same cellular environment; blank for controls.
Quality control
The source processing removed unresolved or incorrectly sized barcode/UMI reads, counted each barcode-by-UMI pair once, and retained only designed barcodes. The paper reports that Pt5C N2 and N3 lentiMPRA samples failed QC; those six source files are preserved in raw_data but omitted here, leaving 18 human-WTC/HS1-11 and chimpanzee-Pt2A RNA/DNA sample pairs. For this package, RNA counts were restricted to barcodes detected in the matched DNA file, normalized to counts per million within each molecule library, summed across tiled oligos, and converted to log2(RNA/DNA). Elements were retained when at least five DNA barcodes were detected in at least half of the 18 retained sample pairs; all 1,866 elements passed this filter. The table does not reproduce the paper's limma prep-date batch correction or differential-testing q-values.
Curation notes
The study spans two cellular organisms and two developmental stages, so no single target-organism or biosample CURIE accurately represents the full table. The paper's final text emphasizes permutations of 2xHAR.164, 2xHAR.170, and 2xHAR.238, while the GEO-deposited permutation files contain additional parent HARs; those belong to the separate permutation experiment. Pt5C main-library files remain available for audit but are not used in this processed table.