AIS risk-variant integrated lentiMPRA in SW1353 chondrocytes
Massively parallel characterization of adolescent idiopathic scoliosis risk variantsA lentivirus-delivered library of 200-bp candidate regulatory sequences tested reference and alternate alleles at AIS-associated variant positions in the human chondrocyte line SW1353. DNA and RNA barcode counts from three biological replicates were used to derive allele-specific reporter activity for the released variant-pair rows.
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; AIS lentiMPRA library, 48 h post-transduction
Each 200-bp candidate regulatory sequence placed the tested allele at base pair 101 and was constructed with a minimal promoter and 15-bp random barcode in a pLS-SceI-derived lentiMPRA vector. SW1353 cells were infected in triplicate at approximately MOI 100; matched genomic DNA and RNA were collected 48 h after infection, barcode reads were processed with MPRAflow, and the paper used MPRAnalyze for quantitative and reference-versus-alternate comparative testing. The released count matrices provide up to 500 barcode indices per allele per biological replicate.
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 · 33 definitions
- element_id
- GEO seq_id identifying the reference and alternate CRS pair.
- chromosome
- Chromosome from the hg19 coordinate in element_id.
- position_hg19
- Variant coordinate on hg19.
- reference_allele
- Reference allele sequence in the CRS pair; '-' denotes an insertion/deletion representation.
- alternate_allele
- Alternate allele sequence in the CRS pair; '-' denotes a deletion representation.
- variant_class
- SNP when both alleles are one base; otherwise INDEL.
- ref_dna_mean_count
- Mean summed DNA barcode count across the three replicates for the reference CRS.
- alt_dna_mean_count
- Mean summed DNA barcode count across the three replicates for the alternate CRS.
- ref_rna_mean_count
- Mean summed RNA barcode count across the three replicates for the reference CRS.
- alt_rna_mean_count
- Mean summed RNA barcode count across the three replicates for the alternate CRS.
- ref_dna_total_count
- Summed DNA barcode count across all three replicates for the reference CRS.
- alt_dna_total_count
- Summed DNA barcode count across all three replicates for the alternate CRS.
- ref_rna_total_count
- Summed RNA barcode count across all three replicates for the reference CRS.
- alt_rna_total_count
- Summed RNA barcode count across all three replicates for the alternate CRS.
- ref_dna_barcode_support
- Number of the 500 barcode indices with any reference DNA count in the three replicates.
- alt_dna_barcode_support
- Number of the 500 barcode indices with any alternate DNA count in the three replicates.
- ref_rna_barcode_support
- Number of the 500 barcode indices with any reference RNA count in the three replicates.
- alt_rna_barcode_support
- Number of the 500 barcode indices with any alternate RNA count in the three replicates.
- ref_joint_barcode_support
- Reference barcode indices with both DNA and RNA signal pooled across the three replicates.
- alt_joint_barcode_support
- Alternate barcode indices with both DNA and RNA signal pooled across the three replicates.
- ref_activity_log2_rep1
- Library-size-normalized log2 RNA/DNA activity for the reference CRS in replicate 1, using a 0.5 count pseudocount.
- ref_activity_log2_rep2
- Library-size-normalized log2 RNA/DNA activity for the reference CRS in replicate 2, using a 0.5 count pseudocount.
- ref_activity_log2_rep3
- Library-size-normalized log2 RNA/DNA activity for the reference CRS in replicate 3, using a 0.5 count pseudocount.
- alt_activity_log2_rep1
- Library-size-normalized log2 RNA/DNA activity for the alternate CRS in replicate 1, using a 0.5 count pseudocount.
- alt_activity_log2_rep2
- Library-size-normalized log2 RNA/DNA activity for the alternate CRS in replicate 2, using a 0.5 count pseudocount.
- alt_activity_log2_rep3
- Library-size-normalized log2 RNA/DNA activity for the alternate CRS in replicate 3, using a 0.5 count pseudocount.
- ref_activity_log2_mean
- Mean of the three reference CRS log2 RNA/DNA activity values.
- alt_activity_log2_mean
- Mean of the three alternate CRS log2 RNA/DNA activity values.
- alt_minus_ref_log2_activity
- Mean alternate-minus-reference log2 RNA/DNA activity; positive values indicate higher alternate activity.
- alt_minus_ref_log2_activity_sd
- Sample standard deviation across the three replicate alternate-minus-reference activity differences.
- effect_direction
- Direction of the count-derived alternate-minus-reference activity effect.
- qc_pass
- True for rows retained after package QC.
- source_accession
- GEO series accession supplying the DNA and RNA count matrices.
Quality control
The authors aligned barcode-association reads with Bowtie 2 and retained exact CRS matches, barcodes uniquely assigned to a CRS at least 70% of the time, and barcode associations with at least three instances. Barcode counting required an exact 15-bp barcode and retained CRSs with at least 10 associated barcodes having observable DNA and RNA reads. Reported mean replicate correlations were 87.33% for DNA and 77% for RNA, with approximately 98% DNA, 96% RNA, and 92% RNA/DNA correlation after CRS-level aggregation. MPRAnalyze used p <= 0.05 versus negative controls for activity and FDR <= 0.10 for allele differences. Package QC retained 4,401 of 4,468 released variant-pair rows: both alleles had finite, nonzero DNA and RNA aggregates in all three replicates and at least 10 barcode indices with both DNA and RNA signal pooled across replicates. The table contains count-derived log2 activity summaries and does not recreate MPRAnalyze p-values or FDRs.
Curation notes
SW1353 is resolved to Cellosaurus CVCL:0543. The GEO count release contains 4,468 complete variant-pair rows plus several classes of controls; this package intentionally keeps variant pairs only because the requested table is for allele-specific variant effects. The original study designed 4,708 testable pairs at 1,664 variant positions, but 4,468 pairs remained after the authors' incomplete/zero-count filtering. The GEO seq_id values provide hg19 coordinates and allele strings but not rsIDs; rsID labels were not inferred, and synthetic alternate alleles are retained. Activity values are derived from the released 500-barcode count subset with sample-level library-size normalization and a 0.5 pseudocount; they are not the paper's MPRAnalyze alpha, log-fold-change, p-value, or FDR outputs.