Experiment / E7EWIHJULEpisomal Plasmid MPRA

SK-N-SH APA variant MPRA

Deciphering the impact of genetic variation on human polyadenylation using APARENT2

An episomal mCherry reporter MPRA tested reference and variant 250-nt oligo libraries containing PAS-centered sequences in SK-N-SH cells. Cleavage profiles were measured by UMI-collapsed paired-end MiSeq RNA sequencing for two biological replicates; the table reports proximal cleavage log-odds ratios and APARENT2 predictions.

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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:0531
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Two separate 250-nt Twist oligo pools (reference and variant) were cloned 25 nt upstream of the bGH poly(A) signal in an mCherry reporter using In-Fusion assembly. SK-N-SH cells were transfected with Lipofectamine 3000; poly(A)+ mRNA was reverse-transcribed with an anchored polyT/UMI primer, sequenced on an Illumina MiSeq (read 1, 292 nt; read 2, 8 nt UMI), and cleavage positions were called from consecutive 20-A runs allowing up to 2 substitutions. Reads without a called proximal polyadenylation site were treated as distal cleavage. The GEO table reports APARENT2 predictions and measured logit/log-odds metrics for the +1 to +51 nt downstream-of-CSE proximal window and for the full proximal interval.

Processed data

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Visible columns (39 of 39)

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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 · 39 definitions

element_id: Unique reference/variant pair identifier derived from the source PAS identifier and variant or condition label.
source_row_index: Zero-based row index from the source GEO CSV file.
gene: Gene symbol associated with the PAS sequence.
gene_id: Source PAS identifier, unique within the gene where available.
library_source: Source/category of the tested sequence in the author-provided library metadata.
library_condition: Source experiment or selection label, such as variant_case, variant_control, or a named control condition.
variant_id: Source SNP identifier when available; blank when the source used a Missing label.
source_variant_label: Exact source snp_id field, including non-rs labels such as Missing or Missing_control.
ref_allele: Reference nucleotide used in the reference reporter sequence.
alt_allele: Alternate nucleotide used in the variant reporter sequence.
chrom: Chromosome in the source genomic coordinate system.
strand: Genomic strand in the source annotation.
pas_pos_hg19: Position of the PAS core hexamer/CSE in hg19; blank for non-genomic control sequences.
pas_pos_hg38: Position of the PAS core hexamer/CSE in hg38; blank when not supplied.
variant_pos_hg19: Variant position in hg19; blank for non-genomic control sequences.
variant_pos_hg38: Variant position in hg38; blank when not supplied.
relative_variant_position: Variant position relative to the PAS CSE, as reported by the source.
ref_sequence_205nt: 205-nt reference sequence used as the APARENT2 input, without reporter homology regions.
var_sequence_205nt: 205-nt variant sequence used as the APARENT2 input, without reporter homology regions.
ref_barcode: Reference reporter barcode sequence.
var_barcode: Variant reporter barcode sequence.
predicted_lor_proximal_1_51nt: APARENT2-predicted log odds ratio for cleavage in the +1 to +51 nt window downstream of the CSE (source delta_logodds_77_127).
predicted_delta_iso_proximal_1_51nt: APARENT2-predicted reference-to-variant difference in proximal isoform abundance in the +1 to +51 nt window, corrected against the 2019 oligo array.
measured_lor_proximal_1_51nt_rep1: Measured variant-versus-reference log odds ratio of proximal cleavage in biological replicate 1.
measured_lor_proximal_1_51nt_rep2: Measured variant-versus-reference log odds ratio of proximal cleavage in biological replicate 2.
measured_lor_proximal_1_51nt_pooled: Measured variant-versus-reference log odds ratio of proximal cleavage after pooling the two biological replicates.
measured_lor_all_proximal_rep1: Measured variant-versus-reference log odds ratio for cleavage anywhere in the proximal PAS interval in biological replicate 1.
measured_lor_all_proximal_rep2: Measured variant-versus-reference log odds ratio for cleavage anywhere in the proximal PAS interval in biological replicate 2.
measured_lor_all_proximal_pooled: Measured variant-versus-reference log odds ratio for cleavage anywhere in the proximal PAS interval after pooling the two biological replicates.
ref_proximal_umi_rep1: Unique UMI count for reference proximal cleavage in biological replicate 1.
ref_proximal_umi_rep2: Unique UMI count for reference proximal cleavage in biological replicate 2.
ref_proximal_umi_pooled: Pooled unique UMI count for reference proximal cleavage.
var_proximal_umi_rep1: Unique UMI count for variant proximal cleavage in biological replicate 1.
var_proximal_umi_rep2: Unique UMI count for variant proximal cleavage in biological replicate 2.
var_proximal_umi_pooled: Pooled unique UMI count for variant proximal cleavage.
ref_total_umi_pooled: Pooled unique UMI count for reference cleavage across proximal and distal products.
var_total_umi_pooled: Pooled unique UMI count for variant cleavage across proximal and distal products.
predicted_lor_all_proximal: APARENT2-predicted log odds ratio for cleavage anywhere in the proximal PAS interval.
predicted_delta_iso_all_proximal: APARENT2-predicted reference-to-variant difference in proximal isoform abundance across the full proximal interval, corrected against the 2019 oligo array.

Quality control

The authors trimmed read 1 adapters with cutadapt v1.15, mapped reads to the known library sequences allowing up to 2 substitutions in the upstream sequence, identified polyadenylation by searching for a consecutive run of 20 A bases with up to 2 substitutions, collapsed mapped reads over read-2 UMIs, and pooled two biological replicates. For this package, rows were retained only when both reference and variant had at least 5 pooled unique UMIs in the +1 to +51 nt downstream-of-CSE window and at least 20 pooled unique UMIs across proximal and distal cleavage. This retained 88 of 100 source rows; the 12 remaining rows were excluded for insufficient proximal or total UMI support.

Curation notes

GEO supplies 100 library rows per cell line, whereas the paper describes 94 clinically relevant PAS SNVs plus 6 previously measured control PASs. Many ASD/de novo entries have no rs identifier; their exact source label is retained in source_variant_label and their element_id is disambiguated with the library condition. The source reports HMC3 elsewhere as HCM3; this experiment uses the GEO/HMC3 name and ATCC HTB-11 SK-N-SH cells. The processed table uses author-provided measured LORs rather than recomputing them and keeps both replicate-specific and pooled values.

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