A lentiviral MPRA used randomly sheared BAC fragments spanning approximately 3 Mb around MAPT to measure cis-regulatory activity in KOLF2.1J h-NGN2 excitatory neurons. The processed table reports activity statistics for 100 bp genomic bins.
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
CL:0000679
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
chr17:43846929-47035962
Perturbation & assay details
Basal / Untreated
Twenty-four human BACs were randomly sheared to an average of approximately 250 bp, cloned into the pLS-SceI lentiMPRA backbone, and associated with 15 bp barcodes. Barcode inserts were assigned to non-overlapping 100 bp hg38 bins; forward and reverse reporter activity was analyzed with MPRAflow and MPRAnalyze. KOLF2.1J h-NGN2 neurons were transduced at day 14 of differentiation and collected at day 18; the GEO series contains three biological replicates per cell type, with replicate 1 represented by merged sequencing runs.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (14 of 14)
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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 · 14 definitions
element_id
Source label for the 100 bp genomic bin.
chromosome
Chromosome reported by the supplementary table.
start_hg38
Bin start coordinate as reported in the source table.
end_hg38
Bin end coordinate as reported in the source table.
element_length_bp
Inclusive bin length derived as end_hg38 minus start_hg38 plus one.
activity_statistic
MPRAnalyze activity statistic for the bin.
z_score
MPRAnalyze z-score.
mad_score
MPRAnalyze median-absolute-deviation score used for activity assessment.
p_value_mad
P-value associated with mad_score.
p_value_zscore
P-value associated with z_score.
significant_p_value_mad_0_05
Whether p_value_mad is at most 0.05.
activity_direction
Direction inferred from the sign of mad_score.
source_table
Supplementary table from which the row was curated.
source_geo_accession
GEO series accession for this MPRA.
Quality control
The authors used MPRAflow barcode association and DNA/RNA counting followed by MPRAnalyze. Package QC retained all 16,200 of 16,200 source rows because each row had a chromosome, valid genomic coordinates, finite activity statistics, and finite pval.mad/pval.zscore values in the expected p-value range. No significance filter was applied, so assay-valid non-significant bins remain available for background modeling.
Curation notes
This child represents the neuronal condition of the BAC MPRA; the matched HEK293FT condition is a separate child experiment. The workbook reports 100 bp bins rather than individual BAC fragment sequences, so element_id and hg38 coordinates are the primary sequence-region identifiers. The large GEO barcode count matrices were not duplicated; the supplementary workbook and small GEO annotation files are included in raw_data.