One condition of the study's transient episomal MPRA. The 61,812-oligo library of Papuan Denisovan/Neanderthal introgressed variants, haplotype-like combinations, positive controls and random negative controls was assayed in GM12878 human lymphoblastoid cells across two usable biological replicates; matched cDNA and plasmid DNA barcode counts were summarized at the oligo level.
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:7526
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The assay used the pMPRA1 plasmid with a GFP reporter and 200-bp oligos consisting of a 170-bp insert flanked by 15-bp cloning adapters and random 15-bp barcodes. Plasmids were transiently nucleofected into lymphoblastoid cell lines; oligo activity was quantified from barcode cDNA relative to plasmid DNA counts. GM12878 was measured in two usable biological replicates.
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 · 54 definitions
oligo_id
Full publisher oligo identifier, including the tested allele or haplotype and library source.
library_id
Variant-level or haplotype-region identifier used to join differential-activity supplementary results.
sequence_class
Sequence class: single_variant or haplotype.
library_group
Publisher-provided library group, including source and single-sequence/haplotype designation.
library_source
Normalized source library: Denisova, Neanderthal, Arensbergen, Tewhey, or random.
test_category
Biological role of the sequence: archaic introgression, positive control, or negative control.
chromosome
Chromosome token parsed from the publisher oligo identifier.
position_hg19
Single-variant coordinate encoded in the oligo identifier on hg19; blank for haplotypes and controls without a single locus.
region_start_hg19
Start coordinate encoded for a haplotype region on hg19; blank for single variants.
region_end_hg19
End coordinate encoded for a haplotype region on hg19; blank for single variants.
rsid
dbSNP rs identifier encoded in the oligo identifier, when available.
allele
Nucleotide carried by a single-variant oligo; blank for haplotypes and random controls.
haplotype_alleles
Haplotype variable-position/allele tokens, such as 82:C|91:G; blank for non-haplotype rows.
haplotype_variant_count
Number of encoded variable sites in the haplotype; blank for non-haplotype rows.
sequence_170bp
S1 sequence with the 15-bp cloning adapters removed, retaining the 170-bp insert.
sequence_length_bp
Length of sequence_170bp in base pairs.
barcode_count
noTags: number of associated barcodes after the author's count filtering.
cell_line
Cell line represented by this experiment table.
replicate_1_id
Usable biological replicate label for the first replicate block.
replicate_1_cDNA_log2_CPM_median
Median barcode cDNA log2 CPM after library-size normalization and count filtering for replicate 1.
replicate_1_pDNA_log2_CPM_median
Median plasmid DNA barcode log2 CPM after library-size normalization and count filtering for replicate 1.
replicate_1_activity_log2_ratio
Median barcode log2(cDNA/pDNA) activity score for replicate 1.
replicate_1_activity_p_value
Author-reported one-sided t-test p-value for replicate 1 activity relative to the replicate background mean.
replicate_1_activity_fdr
Benjamini-Hochberg-adjusted activity p-value for replicate 1.
replicate_1_activity_fdr_pass
Whether replicate 1 activity FDR is below 0.05.
replicate_2_id
Usable biological replicate label for the second replicate block.
replicate_2_cDNA_log2_CPM_median
Median barcode cDNA log2 CPM after library-size normalization and count filtering for replicate 2.
replicate_2_pDNA_log2_CPM_median
Median plasmid DNA barcode log2 CPM after library-size normalization and count filtering for replicate 2.
replicate_2_activity_log2_ratio
Median barcode log2(cDNA/pDNA) activity score for replicate 2.
replicate_2_activity_p_value
Author-reported one-sided t-test p-value for replicate 2 activity relative to the replicate background mean.
replicate_2_activity_fdr
Benjamini-Hochberg-adjusted activity p-value for replicate 2.
replicate_2_activity_fdr_pass
Whether replicate 2 activity FDR is below 0.05.
condition_active_replicate_count
Number of usable GM12878 replicates with activity FDR below 0.05, derived from the replicate pass flags.
condition_active_any
Whether any usable GM12878 replicate has activity FDR below 0.05.
study_active_replicate_count
Number of all five usable study replicates with activity FDR below 0.05, derived from the S2 replicate flags.
study_active_at_least_2_replicates
Study-level active call: whether activity passes in at least two of the five usable study replicates.
snp_differential_tested
Whether a single-variant differential-activity result from S3 was matched to this oligo's variant identifier.
snp_differential_log2FC
S3 mpralm/limma logFC for non-introgressed minus introgressed allele activity; positive indicates higher non-introgressed activity and negative indicates higher introgressed activity.
snp_differential_AveExpr
S3 average expression/activity statistic from the differential-activity model.
snp_differential_t
S3 moderated t statistic for the differential-activity test.
snp_differential_p_value
S3 nominal p-value for the differential-activity test.
snp_differential_fdr
S3 Benjamini-Hochberg-adjusted p-value for the differential-activity test.
snp_differential_B
S3 limma B statistic, the log-odds measure for differential activity.
snp_differential_fdr_pass
Whether the matched S3 differential-activity FDR is below 0.05.
snp_differential_effect_direction
Direction parsed from S3 logFC: introgressed_higher or non_introgressed_higher.
haplotype_anova_tested
Whether an S5 haplotype ANOVA result was matched to this haplotype oligo's region.
haplotype_active_status
S5 region-level activity status for the haplotype.
haplotype_differential_status
S5 region-level differential-activity status, such as Diff Active or Not Diff Active.
haplotype_anova_rep1_p_value
S5 haplotype ANOVA nominal p-value for the first usable haplotype replicate.
haplotype_anova_rep1_fdr
S5 haplotype ANOVA Benjamini-Hochberg-adjusted p-value for the first usable replicate.
haplotype_anova_rep1_fdr_pass
Whether the first usable haplotype ANOVA FDR is below 0.05.
haplotype_anova_rep2_p_value
S5 haplotype ANOVA nominal p-value for the second usable haplotype replicate.
haplotype_anova_rep2_fdr
S5 haplotype ANOVA Benjamini-Hochberg-adjusted p-value for the second usable replicate.
haplotype_anova_rep2_fdr_pass
Whether the second usable haplotype ANOVA FDR is below 0.05.
Quality control
Retained only documented S1 library oligos represented in S2 and with noTags >= 10, matching the author's barcode-count filter; excluded auxiliary QTL-labeled rows present in S2/S5 but absent from the 61,812-oligo S1 library; retained 44,144 rows (37,532 single-variant and 6,612 haplotype rows). Author activity calls use library-size-normalized log2 CPM, per-barcode RNA/DNA activity, one-sided t-tests with Benjamini-Hochberg correction, and activity in at least two usable replicates; 3,894 rows meet that study-level active criterion. The processed table includes both usable GM12878 replicates.
Curation notes
The paper used one shared library in three human lymphoblastoid-cell conditions. This table contains condition-specific GM12878 measurements plus pooled S3 single-variant and S5 haplotype annotations; variant-level S3 statistics are repeated on each corresponding allele oligo, while region-level S5 statistics are repeated on each haplotype allele combination. Supplementary coordinates are labeled hg19, although downstream paper analyses convert coordinates to hg38. The downloaded supplements do not expose explicit reference/alternate or introgressed-state fields, so those labels were not inferred. Auxiliary QTL-labeled rows in S2/S5 were excluded from processed output because they are not present in the documented S1 61,812-oligo library.