The 24,780-oligo library representing reference and alternative alleles for 13,515 candidate 3′-UTR SNPs was assayed in SH-SY5Y human neuroblastoma cells across six independent transfections. Matched plasmid DNA and poly(A) RNA/cDNA UMI counts were used to quantify allele-specific 3′-UTR reporter activity.
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
CVCL:0019
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
PASSPORT-seq used an episomal pIS-0 luciferase reporter. Agilent oligos contained 25 bp upstream and downstream of each reference or alternative allele plus vector-specific assembly sequences; the library contained 24,780 oligos for 13,515 SNPs. Six independent SH-SY5Y transfections were harvested at 42 h for matched DNA and poly(A) RNA extraction. Reporter-specific reverse transcription added an Illumina adapter, a staggered 9–12 nt barcode, and a 10 nt UMI; DNA and cDNA libraries were indexed by transfection and sequenced as 121 nt single-end reads on an Illumina NovaSeq SP lane. Reads were demultiplexed and trimmed, UMIs were used to count unique reads mapped to the 51 nt allele inserts, and edgeR plus a generalized linear mixed model estimated the allele × DNA/cDNA interaction effect (β12).
Processed data
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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 · 27 definitions
oligo_id
GEO pool3 identifier for the tested allele oligo.
library_gene
Gene token embedded in the GEO oligo identifier.
gene
S3 annotated gene containing the tested 3′-UTR SNP.
rsid
dbSNP v151 rs identifier.
reference_allele
Reference allele represented by the oligo.
alternate_allele
Alternative allele represented by the oligo.
chromosome
Chromosome reported in Supplementary Table 3.
position_grch38
SNP position on GRCh38/hg38.
lead_snps
Lead GWAS SNPs whose LD regions overlapped the candidate SNP.
associated_traits
GWAS traits associated with the listed lead SNPs.
ref_dna_mean_count
Mean unique UMI count across six SH DNA replicates for the REF oligo.
alt_dna_mean_count
Mean unique UMI count across six SH DNA replicates for the ALT oligo.
ref_rna_mean_count
Mean unique UMI count across six SH RNA/cDNA replicates for the REF oligo.
alt_rna_mean_count
Mean unique UMI count across six SH RNA/cDNA replicates for the ALT oligo.
dna_alt_frequency
ALT count divided by REF plus ALT count using summed DNA counts across six replicates.
rna_alt_frequency
ALT count divided by REF plus ALT count using summed RNA/cDNA counts across six replicates.
ref_oligo_activity_effect
Published REF oligo RNA/cDNA-versus-DNA activity effect from S3, in the reported model units.
ref_oligo_activity_p_value
Published p-value for REF oligo activity versus DNA.
alt_oligo_activity_effect
Published ALT oligo RNA/cDNA-versus-DNA activity effect from S3, in the reported model units.
alt_oligo_activity_p_value
Published p-value for ALT oligo activity versus DNA.
mpra_variant_effect
Published alternate-versus-reference allele interaction effect β12 for SH-SY5Y.
mpra_p_value
Published p-value for the SH-SY5Y allele interaction effect.
mpra_fdr
Published Benjamini–Hochberg FDR for the SH-SY5Y allele interaction effect.
mpra_significant_fdr_0_05
Boolean indicating whether the published SH-SY5Y MPRA FDR is below 0.05.
mpra_effect_direction
Direction of the alternate allele effect based on the published interaction effect.
replicate_count
Number of independent biological transfections summarized in the means.
source_table
Source supplementary table for the published model and annotation fields.
Quality control
The authors demultiplexed FASTQ files by transfection barcode, trimmed barcode/UMI/primer sequences, mapped the 51 nt insert to reference and alternative oligos, and discarded reads with mismatches or duplicated UMIs (approximately 20% of reads). edgeR generalized linear modeling and an allele × sample-type generalized linear mixed model were used for activity and variant effects, with Benjamini–Hochberg FDR < 0.05 as the paper's significance threshold. Package QC retained 12,173 of 13,515 SH-SY5Y rows: the published SH effect, p-value, and FDR had to be finite with p/FDR in [0,1], and aggregate REF and ALT DNA and RNA UMI counts had to be nonzero across the six biological replicates. The table therefore excludes 1,342 unmodeled or zero-coverage rows while retaining non-significant modeled variants.
Curation notes
The SH-SY5Y line was resolved to Cellosaurus CVCL:0019 (ATCC CRL-2266). The processed table is a variant-level integration of the GEO UMI counts and Supplementary Table 3; it is aligned by rsID and REF/ALT allele pair. The gene token in an oligo_id is retained separately because it differs from the S3 annotated gene for some records. Raw FASTQ reads and the actual oligo sequences were not included because the public MPRA data release provides the UMI count matrix and published variant-level results.