A deep mutational scanning lentiMPRA tested every possible single-nucleotide substitution and a centered 5-bp deletion across a 2,000 bp MAPT promoter region in KOLF2.1J h-NGN2 excitatory neurons. The processed table reports bcalm activity effects relative to matched reference sequences.
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
Variant-focused
Region of interest
chr17:45893536-45895535
Perturbation & assay details
Basal / Untreated
The library used 219 bp oligos centered on every base in the MAPT promoter interval chr17:45893536-45895535, with a reference sequence, three alternate-base sequences, and a centered 5-bp deletion design at each position. Saturation-mutagenesis and ADSP known-variant oligos were combined in a roughly 36,000-oligo pool and separated for analysis. Both insert orientations were combined; length-specific perfect CIGAR barcode association, duplicate-barcode removal, MPRAsnakeflow counting, and bcalm modeling were used in four biological replicates of KOLF2.1J h-NGN2 neurons.
Processed data
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Visible columns (22 of 22)
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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 · 22 definitions
variant_id
Unique source identifier for the alternate or deletion construct.
element_id
Source identifier for the promoter position tested.
chromosome
Chromosome reported by the supplementary table.
position_hg38
Promoter position reported on hg38/GRCh38.
variant_type
Derived mutation class: SNV or 5bp_centered_deletion.
reference_allele
Reference nucleotide for SNVs; blank for the source deletion placeholder.
alternate_allele
Alternate nucleotide for SNVs; blank for the source deletion placeholder.
mutation_descriptor
Human-readable nucleotide substitution or centered_5bp_deletion label.
source_base_ref
Reference allele field copied from the source sheet after converting source NA to blank.
source_base_alt
Alternate allele field copied from the source sheet; deletion rows retain the source deletion label.
design_allele_label
Source design label for the alternate/deletion construct.
log2_fold_change
Published bcalm logFC for the construct relative to its reference sequence.
average_expression
Published average expression value from the model.
t_statistic
Published model t-statistic.
p_value
Published nominal p-value for the construct effect.
adjusted_p_value
Published multiple-testing-adjusted p-value.
b_statistic
Published limma-style B statistic.
significant_fdr_0_05
Whether adjusted_p_value is at most 0.05.
passes_reported_effect_cutoff
Whether adjusted_p_value is at most 0.05 and absolute log2_fold_change exceeds 0.1, matching the paper’s reported effect criterion.
effect_direction
Direction of construct activity relative to the reference sequence.
source_table
Supplementary table from which the row was curated.
source_geo_accession
GEO series accession for this MPRA.
Quality control
The authors compared each alternate base and centered deletion to the corresponding reference sequence using bcalm, with MPRAsnakeflow count generation after length-specific exact barcode mapping and removal of barcodes associated with multiple oligos. Package QC retained 7,996 of 8,000 published mutagenesis rows with finite logFC, P.Value, and adj.P.Val values in the [0,1] p-value range; four rows with missing model statistics were removed. The reported |logFC| > 0.1 and adjusted-p-value threshold is exposed as a flag but was not used to remove non-significant assay-valid variants.
Curation notes
This child represents the neuronal promoter saturation-mutagenesis condition; the matched HEK293FT condition is separate. The raw workbook encodes deletion constructs with base_ref=NA and base_alt=deletion; the processed table recodes these as 5bp_centered_deletion and retains source-base fields for traceability. Reference-control rows are not included in the source result sheet because effects are already reported relative to the reference sequence.