7.5k positive- and negative-control allelic MPRA library across LCLs
Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assayA follow-up 7,500-oligo episomal MPRA library tested 264 positive-control variants from the 79k screen together with location-matched and genome-wide negative controls in NA12878 and NA19239 lymphoblastoid cell lines. The table pairs the deposited allele-A and allele-B rows and reports count-derived RNA-over-DNA activity and allelic differences.
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.
Perturbation & assay details
Basal / Untreated
The smaller follow-up library used the same synthetic oligo/minimal-promoter/GFP reporter architecture and 20-nucleotide 3' UTR barcode strategy as the 79k library. The deposited 7.5k count matrix contains five plasmid-input replicates, five NA12878 RNA replicates, and three NA19239 RNA replicates. The authors additionally downsampled the 7.5k barcode data in their cross-library sensitivity analysis; this package uses the deposited collapsed-count matrix as supplied and does not perform a second barcode-level downsampling.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 30 definitions
- element_id
- Pair identifier formed from the deposited count IDs after removing the central allele-A/B marker; source suffixes such as _RC and _alt-1 are retained.
- variant_id
- Coordinate-style or rsID identifier for the centered variant, with source _RC and _alt-1 suffixes removed.
- variant_type
- SNP for rsID records; indel_or_coordinate_id for coordinate-style insertion/deletion records.
- orientation
- Inferred from the source pair ID: reverse when the pair carries the _RC suffix, otherwise forward.
- neighboring_haplotype
- Inferred source suffix: alt-1 when the pair carries _alt-1, otherwise ref/primary construct; this is not a claim about the centered A/B allele sequence.
- allele_a_oligo_id
- Exact deposited GEO collapsed-count row ID containing the central allele-A marker.
- allele_b_oligo_id
- Exact deposited GEO collapsed-count row ID containing the central allele-B marker.
- qc_status
- Package-level status; only pairs passing the paired plasmid-input threshold are emitted.
- qc_min_dna_count
- Smaller of allele-A and allele-B summed plasmid-input counts across the five deposited plasmid replicates.
- allele_a_dna_count_sum
- Sum of the five unnormalized deposited plasmid-input counts for allele A.
- allele_b_dna_count_sum
- Sum of the five unnormalized deposited plasmid-input counts for allele B.
- allele_a_dna_cpm_mean
- Mean allele-A plasmid-input count per million across the five plasmid replicates, using each sample's total oligo count for normalization.
- allele_b_dna_cpm_mean
- Mean allele-B plasmid-input count per million across the five plasmid replicates, using each sample's total oligo count for normalization.
- allele_a_na12878_rna_count_sum
- Sum of allele-A counts across the five deposited NA12878 RNA replicates.
- allele_b_na12878_rna_count_sum
- Sum of allele-B counts across the five deposited NA12878 RNA replicates.
- allele_a_na12878_rna_cpm_mean
- Mean allele-A NA12878 RNA count per million across the five RNA replicates.
- allele_b_na12878_rna_cpm_mean
- Mean allele-B NA12878 RNA count per million across the five RNA replicates.
- allele_a_na12878_log2_activity
- Derived NA12878 allele-A activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- allele_b_na12878_log2_activity
- Derived NA12878 allele-B activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- na12878_allelic_log2_effect_b_minus_a
- Derived NA12878 allele-B-minus-allele-A activity difference on the log2 scale.
- allele_a_na19239_rna_count_sum
- Sum of allele-A counts across the three deposited NA19239 RNA replicates.
- allele_b_na19239_rna_count_sum
- Sum of allele-B counts across the three deposited NA19239 RNA replicates.
- allele_a_na19239_rna_cpm_mean
- Mean allele-A NA19239 RNA count per million across the three RNA replicates.
- allele_b_na19239_rna_cpm_mean
- Mean allele-B NA19239 RNA count per million across the three RNA replicates.
- allele_a_na19239_log2_activity
- Derived NA19239 allele-A activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- allele_b_na19239_log2_activity
- Derived NA19239 allele-B activity: log2((RNA CPM mean + 1)/(DNA CPM mean + 1)).
- na19239_allelic_log2_effect_b_minus_a
- Derived NA19239 allele-B-minus-allele-A activity difference on the log2 scale.
- allele_a_combined_lcl_log2_activity
- Derived combined-LCL allele-A activity, weighted by the deposited replicate counts: five NA12878 replicates and three NA19239 replicates.
- allele_b_combined_lcl_log2_activity
- Derived combined-LCL allele-B activity, weighted by the deposited replicate counts: five NA12878 replicates and three NA19239 replicates.
- combined_lcl_allelic_log2_effect_b_minus_a
- Derived combined-LCL allele-B-minus-allele-A activity difference on the log2 scale.
Quality control
The authors' barcode reconstruction and read filtering are described in the supplemental experimental procedures; the original follow-up analysis matched the 79k library's expression and allelic-skew calling framework and used downsampling for a specific cross-library comparison. For this package, the 7,500 deposited oligo rows were paired by the embedded central allele marker A or B, yielding 3,750 complete allele pairs. Both alleles were required to have at least 20 summed plasmid-input reads across Plasmid_r1 through Plasmid_r5; 3,704 pairs passed and 46 low-input pairs were excluded. Count-derived activity values are per-sample CPM summaries with a 1-count-on-the-CPM-scale pseudocount. Because this release does not contain the 7.5k author summary statistics workbook, no new significance calls are asserted here.
Curation notes
The raw 7.5k count identifiers encode the central allele as A or B and may carry _RC and _alt-1 source suffixes for orientation/alternate construct variants. The table deliberately labels the contrast A/B rather than asserting reference/alternative nucleotide identity because the 7.5k collapsed-count release does not include a separate allele-annotation table. The authors' 7.5k analysis downsampled barcodes for cross-library comparison; this element-level package retains the deposited count values and reports no re-fit p-values.