A 270-bp differentially accessible (DA) candidate regulatory-element library was tested with lentiMPRA in GW18 primary human cortical cells. Barcode RNA/DNA ratios quantify enhancer activity, with cell-type accessibility, DA, chromatin-loop, ABC, motif, and conservation annotations retained.
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
UBERON:0000956
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; GW18 primary human cortical cells
Twist oligo inserts were 270 bp long and were cloned upstream of a 31-bp minimal promoter and a 15-bp random barcode in a lentiMPRA vector. Lentiviral integration enabled reporter delivery to primary cortical cells; activity is the CPM-normalized RNA/DNA barcode ratio. The source DA library was tested in three primary-cell replicates and includes genomic, chromatin, motif, and predicted target-gene annotations.
Processed data
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Visible columns (19 of 19)
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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 · 19 definitions
element_id
Source insert_name identifying the tested 270-bp regulatory element.
chromosome
Chromosome of the tested insert in GRCh38.
start
Source start coordinate of the tested insert.
end
Source end coordinate of the tested insert.
insert_length_bp
Derived insert length in base pairs, calculated as end minus start.
rna_dna_ratio
Source CPM-normalized reporter RNA divided by DNA barcode activity ratio.
log2_rna_dna_ratio
Derived base-2 logarithm of the RNA/DNA activity ratio.
is_active
Source binary activity call; active sequences exceed the median positive-control activity threshold.
is_silencer
Source primary-cell silencer annotation; 1 indicates a silencer call and 0 indicates no call.
atac_cell_types
Semicolon-separated cell types whose ATAC-seq annotations overlap the insert.
Semicolon-separated H3K27ac evidence sources overlapping the insert.
motif_total_usf
Source count of USF-family motif matches in the insert.
motif_total_all
Source total count of motif matches in the insert.
has_placseq_loop
1 if the insert overlaps a PLAC-seq loop annotation, otherwise 0.
has_pchic_loop
1 if the insert overlaps a promoter-capture Hi-C loop annotation, otherwise 0.
loop_target_genes
Unique promoter target genes aggregated from the source chromatin-loop annotations.
abc_target_genes
Unique target gene names from Activity-by-Contact annotations.
conservation_mean
Source mean evolutionary conservation score for the insert.
Quality control
The supplemental methods required merged reads with a 270M CIGAR, mapping quality >30 for DA reads, base quality >=30, barcode Shannon entropy >0.5, barcode observation >=3 times with >=90% assignment to the same insert, >=10 unique barcodes per insert, and >=40 total DNA barcodes. DNA/RNA counts were CPM-normalized and activity was RNA/DNA; the source reports a median of 56 barcodes per DA insert and approximately 0.93 replicate Pearson correlation. Data S1 contains 46,370 post-QC primary DA inserts; all were retained here after requiring finite coordinates, a finite nonnegative activity ratio, and an is_active value.
Curation notes
This table is the QC-passed DA-region library rather than a list of GWAS variants. The biosample is represented at the cerebral-cortex tissue level because the assay contains mixed primary cortical cell types and no single terminal Cell Ontology type. Source Data S1 primary rows were retained one-for-one after the documented finite-value checks; no source rows failed those additional checks.