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Experiment / E55X60OOKIntegrated lentiMPRA

Permutation HAR lentiMPRA library

Machine learning dissection of human accelerated regions in primate neurodevelopment

A separate lentiMPRA library tested designed evolutionary intermediates between chimpanzee and human HAR alleles, together with the deposited controls. The available count files cover human WTC and chimpanzee Pt2A iPSC-derived neural cells at N2 and N3 stages, with three technical replicates per condition.

Download processed table (CSV)Raw source dataAPI 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
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

Permutation oligos were generated by introducing all tested combinations of human alleles into the chimpanzee sequence background, then assayed with the same 171-bp lentiviral barcode reporter, 15-bp designed barcodes, 10-bp UMIs, and matched RNA/DNA readout as the main library. The deposited permutation annotations preserve the parent HAR, permutation number, and human/chimpanzee base changes.

Processed data

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

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 combining parent HAR and permutation number, or a control identifier.
element_name
Parent HAR name or control annotation.
element_class
Permutation, Positive control, Negative control, or Control.
sequence_species
Blank because permutation constructs are mixed evolutionary intermediates rather than a single species allele.
parent_har
Parent HAR from which a permutation was generated.
permutation_index
Ordinal permutation number in the deposited construct design.
permutation_total
Total number of possible permutations in the deposited parent-HAR design.
variant_description
Comma-separated original annotation of the tested human/chimpanzee base changes.
coordinates_hg19
Tested hg19 coordinate(s) when present in the original construct annotation; blank when the permutation annotation does not include coordinates.
oligo_count
Number of distinct construct annotations 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.
sample_label
Normalized sample label combining cell species, cell line, stage, and technical replicate.
source_dataset
GEO subseries supplying the count files.
cell_species
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
Permutation HAR 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
Blank for the permutation library because each row is an evolutionary intermediate rather than a paired human/chimpanzee allele.

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. RNA counts were restricted to barcodes detected in the matched DNA file, normalized to counts per million within each molecule library, and converted to log2(RNA/DNA) after aggregation across contributing oligos. Elements were retained when at least five DNA barcodes were detected in at least half of the 12 deposited permutation-library sample pairs; all 1,003 elements passed this filter. The table reflects the available WTC and Pt2A permutation files and does not infer missing HS1-11 or Pt5C permutation measurements.

Curation notes

The published Methods section describes the permutation work around three selected HARs, whereas the pre-existing GEO count deposit contains permutation constructs for seven parent HARs and only WTC/Pt2A cellular samples. The table preserves the full available deposited permutation set (including controls) and records the exact construct-level variant annotation in variant_description/representative_annotation.

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