A variant-focused lentiMPRA tested Alzheimer’s Disease Sequencing Project insertions and deletions overlapping MAPT-proximal candidate regulatory regions in KOLF2.1J h-NGN2 excitatory neurons. The processed table reports alternate-versus-reference activity effects from the published bcalm analysis.
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
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The combined variation library used 219 or 218 bp oligos centered on ADSP InDels and included variants of no more than 10 bp, matched reference sequences, promoters, and negative controls. The library was cloned into the lentiMPRA backbone and assayed in four biological replicates of KOLF2.1J h-NGN2 neurons; barcode associations used length-specific perfect CIGAR matches, multiple-oligo barcodes were removed, and MPRAsnakeflow counts were analyzed with bcalm. The table contains the InDel subset of the combined variation/mutagenesis pool and compares alternate sequence to reference sequence.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (18 of 18)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Page 1 · 50 rows · More results available
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 18 definitions
variant_id
Source element identifier encoding the tested InDel and genomic allele change.
variant_type
Variant class, InDel.
chromosome
Chromosome reported by the supplementary table.
position_hg38
Variant position reported on hg38/GRCh38.
reference_allele
Reference sequence allele in the source element identifier.
alternate_allele
Inserted or deleted alternate sequence in the source element identifier.
mutation_descriptor
Reference-to-alternate sequence change, formatted as REF>ALT.
log2_fold_change
Published bcalm logFC for alternate versus reference reporter activity.
average_expression
Published average expression value from the model.
t_statistic
Published model t-statistic.
p_value
Published nominal p-value for the alternate-versus-reference 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 alternate 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 excluded InDels greater than 10 bp and variants with allele count 0, used length-specific exact barcode mapping, removed barcodes associated with multiple oligos, and analyzed the DNA/RNA counts with bcalm. Package QC retained 586 of 603 published InDel rows with finite logFC, P.Value, and adj.P.Val values in the [0,1] p-value range; 17 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 contains the neuronal InDel results from the combined variation MPRA; the matched HEK293FT condition is separate. The supplementary result sheet does not provide dbSNP rs identifiers, so the coordinate-and-allele-bearing source element identifier is retained. Rows with missing bcalm model statistics were excluded, while non-significant but modeled variants remain.