An episomal UMI-STARR-seq library containing 170-bp sequences centered on severe COVID-19-associated variants, both reference and alternate alleles, and all possible allelic combinations for variants within 100 bp was screened in untreated human A549 lung adenocarcinoma cells. Plasmid DNA input and polyadenylated RNA output were measured across biological replicates to quantify enhancer activity and allele-specific effects.
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:0023
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal hSTARR screening vector (Addgene #99296) following the UMI-STARR-seq protocol. The library contained 9,788 single-variant oligos, 3,776 combinatorial oligos, and 238 controls before filtering; candidate inserts were 170 bp with 15-bp cloning adapters. A549 cells were electroporated with the pooled library, harvested after 6 h, and assayed with two DNA input and five polyadenylated-RNA output biological replicates. UMI-collapsed sequence counts were analyzed as RNA-over-DNA log2 fold-change with DESeq2, and allele contrasts were assessed with mpralm.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (55 of 55)
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 · 55 definitions
oligo_id
Unique pooled-library oligo identifier from the S1 FASTA and S2 activity table.
sequence_category
Paper S2 category: Covid_GWAS, Pos_ctrl_A549, Pos_ctrl_H358, or Neg_ctrl.
library_design
Package classification as single_variant, variant_combination, or control.
control_region
Chromosomal interval parsed from a control oligo ID; blank for non-controls.
variant_count
Number of variants represented by the oligo; one for single-variant oligos and the component count for combinations.
variant_id
Normalized identifier for a single variant: the reported rsID when available, otherwise chr:position.
source_variant_label
Exact S3 rsID field, including coordinate-only labels used by the source for variants without an rsID.
component_variant_ids
Semicolon-separated normalized identifiers for combination components, resolved from S3 by position and allele when possible and otherwise represented by chr:position.
variant_positions
Single chr:position or semicolon-separated component positions in the oligo.
allele_combination
Single-variant ref/alt state or the tested component alleles joined with | for combinations.
allele_state
Reference or alternate for single oligos, combination for multi-variant oligos, and control for controls.
chromosome
Chromosome label from S3, a component identifier, or a control interval.
oligo_start
Published S3 oligo start for single variants, parsed control start, or inferred minimum component position minus 85 bp for combinations.
oligo_end
Published S3 oligo end for single variants, parsed control end, or inferred maximum component position plus 85 bp for combinations.
coordinate_source
Provenance of interval coordinates: published S3, control ID, or derived from component coordinates and the 170-bp design.
reference_allele
Reference allele reported in S3 for single variants.
alternative_allele
Alternative/risk allele reported in S3 for single variants.
tested_allele
Actual nucleotide or indel sequence represented by this single-variant oligo, from S3.
library_sequence
Full S1 library sequence, including the 15-bp forward and reverse cloning adapters.
insert_sequence
S1 library sequence with the known 15-bp adapters removed; preserves the source case convention marking variant bases.
insert_length_bp
Length in bases of insert_sequence, allowing for source indel constructs.
gc_content_percent
GC percentage of the tested insert; published S3 value for single variants and S1-derived calculation otherwise.
gc_content_source
Whether GC content came from published S3 or was derived from the S1 insert.
nearest_tss_gene
Nearest TSS gene reported in S3 for single variants.
distance_to_nearest_tss_bp
Distance in base pairs to the nearest TSS reported in S3 for single variants.
log2_activity
S2 DESeq2 log2 fold-change of normalized output RNA over input DNA.
activity_fdr
S2 DESeq2 Benjamini-Hochberg adjusted p-value for output-versus-input activity.
input_average_normalized_count
S2 normalized plasmid DNA input count averaged across input replicates.
output_average_normalized_count
S2 normalized RNA output count averaged across output replicates.
paper_activity_call
Derived paper threshold call: active when log2_activity > 1 and activity_fdr < 0.01, otherwise inactive.
single_log2fc_deseq2
S3 DESeq2 output-versus-input log2 fold-change for the single-variant oligo.
single_fdr_deseq2
S3 DESeq2 adjusted p-value for the single-variant oligo.
allelic_log2fc_mpralm
S3 mpralm alternative-versus-reference allele effect, repeated on both allele rows for the variant.
allelic_fdr_mpralm
S3 mpralm adjusted p-value for the allele contrast.
allele_result
S3 single-variant classification: Inactive, Active only, Allele-specific only, or amVar.
rna_dna_ratio_rep1
S3 RNA/DNA activity ratio for biological replicate 1.
rna_dna_ratio_rep2
S3 RNA/DNA activity ratio for biological replicate 2.
rna_dna_ratio_rep3
S3 RNA/DNA activity ratio for biological replicate 3.
rna_dna_ratio_rep4
S3 RNA/DNA activity ratio for biological replicate 4.
rna_dna_ratio_rep5
S3 RNA/DNA activity ratio for biological replicate 5.
pair_id
Common chr_position1_position2 identifier for a two-variant combination represented in S4/S5.
pair_ref_ref_log2fc
Published S5 activity for the reference-reference allelic combination.
pair_ref_alt_log2fc
Published S5 activity for the reference-alternate allelic combination.
pair_alt_ref_log2fc
Published S5 activity for the alternate-reference allelic combination.
pair_alt_alt_log2fc
Published S5 activity for the alternate-alternate allelic combination.
pair_expected_alt_alt_additive_log2fc
Published S5 expected alternate-alternate activity under the additive model.
pair_expected_alt_alt_multiplicative_log2fc
Published S5 expected alternate-alternate activity under the multiplicative model.
pair_interaction_additive
Published S5 observed-minus-expected alternate-alternate discrepancy under the additive model.
pair_interaction_multiplicative
Published S5 observed-minus-expected alternate-alternate discrepancy under the multiplicative model.
pair_min_pairwise_adj_p
Minimum adjusted p-value among the six S4 pairwise allele comparisons.
pair_significant_comparisons
Semicolon-separated S4 comparisons with adjusted p < 0.05, annotated with their adjusted p-value.
alphagenome_prediction_count
Number of matching S6 AlphaGenome feature predictions for the single variant.
alphagenome_classes
S6 prediction classes, such as emVar or non_emVar, joined with semicolons.
alphagenome_feature_summary
Compact semicolon-separated S6 feature summaries containing assay, gene/TF/mark, class, raw score, and quantile score; the full source table is in raw_data.
qc_pass
TRUE for every row retained in the authors' deposited post-QC S2 activity table.
Quality control
The authors assessed sequencing quality with FastQC, aligned uniquely to a custom library reference with Bowtie1, removed PCR duplicates using UMI-tools, and counted sequences with HTSeq. They required at least 10 UMI-collapsed reads in each of the two input replicates and at least 5 in each of the five output replicates; 13,461 post-QC sequence rows are deposited in the S2/GEO activity table and retained here. The paper called sequences active when log2FC > 1 and FDR < 0.01, and called amVars when the mpralm allele FDR was < 0.01 and at least one allele was active. table.csv contains exactly the deposited post-QC S2 rows, including controls, with no additional row filtering.
Curation notes
This is one untreated A549 STARR-seq experiment whose pooled library contains both single-variant alleles and multi-variant combinations, so one table is used for all post-QC library oligos. The S3 workbook contains eight exact duplicate rows for repeated oligo IDs; enrichment deduplicated only those identical annotations while table.csv retains one row per unique S2 oligo. The S1 FASTA has six duplicate H358 control headers with identical sequences. Combination intervals are derived from their component identifiers and the stated 170-bp design only where marked in coordinate_source. S2_all_library_activity.xlsx and the GEO supplementary workbook are byte-identical copies of the deposited all-library activity results. No raw sequencing reads are included; GEO/SRA links are preserved in the study metadata and GEO family file.