A 59,976-oligo library containing 34,344 bi-allelic variant targets and 265 control regions was tested in triplicate in hTERT-immortalized human aortic endothelial cells. This nonstimulated condition was harvested after the common transfection interval and quantified by poly(A) RNA relative to the shared input plasmid DNA library.
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:Z065
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated (mock treatment)
Episomal hSTARR-seq_ORI reporter plasmid (Addgene 99296) with 198-bp enhancer inserts, a 2-bp library barcode and the native STARR-seq polyadenylation/readout configuration. The library was electroporated into teloHAECs with the Neon system; three biological replicates were sequenced on an Illumina NextSeq 500 after UMI-tagged reverse transcription and junction PCR. RNA/DNA activity is represented for GEO samples GSM5471936, GSM5471937 and GSM5471938 against shared input-DNA samples GSM5471945-GSM5471947.
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 · 50 definitions
oligo_id
Stable identifier derived from the source region, 2-bp barcode and a sequence hash.
element_id
Tested library region as chr:start-end, or the source scrambled-control name when coordinates are NA.
chromosome
Chromosome or source sequence label from the GEO matrix.
start_hg19
Inclusive hg19 region start coordinate; null for scrambled controls.
end_hg19
Inclusive hg19 region end coordinate; null for scrambled controls.
sequence_length_bp
Length of the tested insert sequence in base pairs.
oligo_index_in_element
1-based source-order index for an oligo within its tested region.
allelic_identity_barcode
Two-base library barcode supplied in the GEO matrix; it is not interpreted as a genomic reference or alternate allele.
enhancer_sequence
Synthetic 198-bp-class sequence insert tested by STARR-seq.
gc_fraction
Fraction of sequence bases that are G or C.
control_status
Scrambled-sequence control label when the source chromosome is random_scrambled_seq_*; null otherwise.
region_haplotype_count
Number of source oligo rows sharing the region coordinates.
region_haplotype_count_qc
Number of oligo rows for this region passing the condition-specific nonzero-count QC filter.
published_s2_high_confidence
TRUE when the region overlaps one or more of the 89 high-confidence SNPs in Supplemental Table S2.
published_s2_rs_ids
Semicolon-separated high-confidence rsIDs from Supplemental Table S2 whose hg19 positions fall inside the region; null when none are mapped.
published_s2_variant_ref_alt
Semicolon-separated reference>alternate alleles for mapped Supplemental Table S2 SNPs.
published_s2_positions_hg19
Semicolon-separated hg19 positions for mapped Supplemental Table S2 SNPs.
published_s2_eqtl_genes
Paper-supplied eQTL gene annotations from Supplemental Table S2.
published_s2_molqtl
Paper-supplied molecular-QTL annotations from Supplemental Table S2.
published_s2_motif_mutated_pwm
Paper-supplied PWM motif mutation annotations from Supplemental Table S2.
published_s2_svm_tf_disruption
Paper-supplied predicted TF disruption annotations from Supplemental Table S2.
published_s2_gwas_traits
Paper-supplied GWAS trait annotations from Supplemental Table S2.
published_s2_starr_pvalue_0h
Paper-supplied STARR-seq allele-specific p-value at 0 h for mapped Supplemental Table S2 SNPs; not recomputed.
published_s2_starr_pvalue_6h
Paper-supplied STARR-seq allele-specific p-value at 6 h for mapped Supplemental Table S2 SNPs; not recomputed.
published_s2_starr_pvalue_24h
Paper-supplied STARR-seq allele-specific p-value at 24 h for mapped Supplemental Table S2 SNPs; not recomputed.
published_s2_higher_expression_allele_0h
Paper-supplied higher-expression allele at 0 h for mapped Supplemental Table S2 SNPs.
published_s2_higher_expression_allele_6h
Paper-supplied higher-expression allele at 6 h for mapped Supplemental Table S2 SNPs.
published_s2_higher_expression_allele_24h
Paper-supplied higher-expression allele at 24 h for mapped Supplemental Table S2 SNPs.
dna_count_rep1
UMI-deduplicated input plasmid DNA count for input replicate 1.
dna_count_rep2
UMI-deduplicated input plasmid DNA count for input replicate 2.
dna_count_rep3
UMI-deduplicated input plasmid DNA count for input replicate 3.
dna_count_sum
Sum of the three input plasmid DNA counts.
rna_count_rep1
UMI-deduplicated poly(A) reporter RNA count for untreated replicate 1.
rna_count_rep2
UMI-deduplicated poly(A) reporter RNA count for untreated replicate 2.
rna_count_rep3
UMI-deduplicated poly(A) reporter RNA count for untreated replicate 3.
rna_count_sum
Sum of the three untreated reporter RNA counts.
dna_cpm_rep1
Input DNA count per million source-matrix reads for replicate 1.
dna_cpm_rep2
Input DNA count per million source-matrix reads for replicate 2.
dna_cpm_rep3
Input DNA count per million source-matrix reads for replicate 3.
rna_cpm_rep1
Untreated reporter RNA count per million source-matrix reads for replicate 1.
rna_cpm_rep2
Untreated reporter RNA count per million source-matrix reads for replicate 2.
rna_cpm_rep3
Untreated reporter RNA count per million source-matrix reads for replicate 3.
log2_rna_dna_rep1
Library-size-normalized log2 RNA/DNA activity ratio for replicate 1.
log2_rna_dna_rep2
Library-size-normalized log2 RNA/DNA activity ratio for replicate 2.
log2_rna_dna_rep3
Library-size-normalized log2 RNA/DNA activity ratio for replicate 3.
mean_log2_rna_dna
Mean of the three library-size-normalized log2 RNA/DNA activity ratios.
mean_normalized_rna_dna_ratio
Arithmetic mean of the three normalized RNA/DNA activity ratios.
sd_log2_rna_dna
Sample standard deviation of the three replicate log2 RNA/DNA activity ratios.
activity_rank
Descending rank of mean_log2_rna_dna among QC-passing oligos in this experiment.
qc_status
PASS for rows meeting the nonzero-count filter in all three input-DNA and all three untreated RNA replicates.
Quality control
Applied the authors' stated mpralm input filter: retained a library oligo only when all three input-DNA replicates and all three condition RNA replicates had at least one UMI-deduplicated count. This yielded 58,904 of 59,976 source oligos; the retained RNA log2(count+1) replicate Pearson correlations were 0.9199, 0.9368 and 0.9214. The source processing already required valid UMIs, unique and strand-specific mapping, UMI deduplication and featureCounts; no additional count threshold was imposed.
Curation notes
The public GEO matrix is the authors' UMI-deduplicated oligo-level count matrix, not the complete internal variant-to-allele aggregation table. Therefore table.csv reports sequence/region/haplotype-level RNA/DNA activity; the 89 high-confidence SNP annotations and their paper-supplied STARR-seq p-values from Supplemental Table S2 are attached where their hg19 position falls within a tested region. The 2-bp allelic_identity_barcode is retained as a source library barcode and is not interpreted as the genomic allele. Scrambled controls have NA coordinates and are retained when they pass QC.