Multiplexed mSTARR-seq allele-specific regulatory effects
Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomesThe same paired methylated and unmethylated mSTARR-seq libraries were used to compare reference- versus alternate-allele reporter output across naturally occurring variants carried by the multiplexed donor genomes. The table contains the 1,359 sites qualified for cross-condition ASE modeling, condition-specific beta-binomial results, source mashr results where published, and derived reference/alternate count summaries.
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
M.SssI-induced CpG methylation versus water/mock (sham) treatment
This is the allele-specific analysis of the multiplexed mSTARR-seq assay. Individual-specific CpG-free barcodes identify DNA fragments from 25 diverse 1000 Genomes donors, while reporter RNA is compared with plasmid DNA separately in methylated and unmethylated K562 transfections. The authors used GATK-based SNP calling/joint genotyping and beta-binomial models with sample type and pool as covariates; mashr compared effect estimates across methylation states. The processed rows use the source coordinate identifiers and do not claim an rsID or allele base that is not present in the retained model/ASE files.
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 · 41 definitions
- variant_site
- Source coordinate-based variant identifier, formatted as chromosome_position; no rsID or allele bases are implied.
- chromosome
- Chromosome parsed from variant_site.
- position_hg38
- Variant position parsed from variant_site in the GRCh38/hg38 coordinate system.
- methylated_ase_beta
- Source beta-binomial methylated-condition effect estimate comparing reference/alternate representation between reporter RNA and plasmid DNA.
- methylated_ase_se
- Standard error of the methylated-condition ASE effect estimate.
- methylated_ase_pvalue
- Raw P-value for the methylated-condition beta-binomial ASE test.
- methylated_ase_q
- Source FDR-adjusted P-value for the methylated-condition ASE test.
- methylated_ase_status
- Authors' methylated-condition ASE call: significant or not_significant.
- unmethylated_ase_beta
- Source beta-binomial unmethylated-condition effect estimate comparing reference/alternate representation between reporter RNA and plasmid DNA.
- unmethylated_ase_se
- Standard error of the unmethylated-condition ASE effect estimate.
- unmethylated_ase_pvalue
- Raw P-value for the unmethylated-condition beta-binomial ASE test.
- unmethylated_ase_q
- Source FDR-adjusted P-value for the unmethylated-condition ASE test.
- unmethylated_ase_status
- Authors' unmethylated-condition ASE call: significant or not_significant.
- condition_effect_difference
- Source sign field from ASEmashr_inputsites, carrying the authors' methylated-versus-unmethylated ASE effect comparison value without transformation.
- ase_direction_concordance
- Source direction label describing whether the condition-specific ASE effects have the same or opposite direction.
- methylated_ase_beta_for_mashr
- Source transformed methylated-condition ASE beta supplied to the mashr analysis.
- unmethylated_ase_beta_for_mashr
- Source transformed unmethylated-condition ASE beta supplied to the mashr analysis.
- mashr_output_present
- Boolean indicating whether the site is present in the published 783-row ASE_mashr_results file.
- mashr_methylated_posterior_effect
- Published mashr posterior mean for the methylated-condition ASE effect, when output is present.
- mashr_unmethylated_posterior_effect
- Published mashr posterior mean for the unmethylated-condition ASE effect, when output is present.
- mashr_methylated_lfsr
- Published mashr local false sign rate for the methylated-condition ASE effect, when output is present.
- mashr_unmethylated_lfsr
- Published mashr local false sign rate for the unmethylated-condition ASE effect, when output is present.
- methylation_ase_log2_fc
- Published mashr log2 contrast between the methylated and unmethylated ASE effects, when output is present.
- methylation_ase_status
- Published ASE mashr call MD or not_MD for 783 strong-ASE sites; not_in_published_mashr_output for the other 576 qualified cross-condition sites.
- methylated_dna_total_mean
- Mean total allele count across the five released methylated DNA replicates.
- methylated_dna_reference_mean
- Mean source reference-allele count across the five released methylated DNA replicates.
- methylated_dna_alternate_mean
- Mean alternate-allele count across the five released methylated DNA replicates, derived as total count minus reference count per replicate.
- methylated_dna_replicates_with_both_alleles
- Number of released methylated DNA replicates with both source reference count and derived alternate count greater than zero.
- unmethylated_dna_total_mean
- Mean total allele count across the six released unmethylated DNA replicates.
- unmethylated_dna_reference_mean
- Mean source reference-allele count across the six released unmethylated DNA replicates.
- unmethylated_dna_alternate_mean
- Mean alternate-allele count across the six released unmethylated DNA replicates, derived as total count minus reference count per replicate.
- unmethylated_dna_replicates_with_both_alleles
- Number of released unmethylated DNA replicates with both source reference count and derived alternate count greater than zero.
- methylated_rna_total_mean
- Mean total allele count across the five released methylated RNA replicates.
- methylated_rna_reference_mean
- Mean source reference-allele count across the five released methylated RNA replicates.
- methylated_rna_alternate_mean
- Mean alternate-allele count across the five released methylated RNA replicates, derived as total count minus reference count per replicate.
- methylated_rna_replicates_with_both_alleles
- Number of released methylated RNA replicates with both source reference count and derived alternate count greater than zero.
- unmethylated_rna_total_mean
- Mean total allele count across the six released unmethylated RNA replicates.
- unmethylated_rna_reference_mean
- Mean source reference-allele count across the six released unmethylated RNA replicates.
- unmethylated_rna_alternate_mean
- Mean alternate-allele count across the six released unmethylated RNA replicates, derived as total count minus reference count per replicate.
- unmethylated_rna_replicates_with_both_alleles
- Number of released unmethylated RNA replicates with both source reference count and derived alternate count greater than zero.
- coverage_qc_passed
- Boolean indicating that the site passed the authors' cross-condition coverage/variability filter; true for every row in this table.
Quality control
The authors first restricted ASE analysis to active regulatory windows containing only one SNP or haplotype, retaining 8,570 variants in the unmethylated condition and 5,853 in the methylated condition. For methylation-dependent genetic effects they retained 1,359 sites with adequate coverage and variability to be modeled in both conditions, excluding monoallelic/nearly monoallelic sites from this cross-condition set. They used beta-binomial models on reference and alternate allele counts with pool as a covariate and a 1% FDR significance label. The source cross-condition input contains 1,359 qualified sites; the published ASE mashr result file contains 783 strong-ASE sites, of which 575 are MD and 208 are not_MD, while 576 qualified input sites have no row in that published output. All 1,359 rows pass the source cross-condition QC and are retained; missing mashr output is explicitly marked rather than treated as a failed assay.
Curation notes
This child table is an analysis layer of the same wet-lab assay as the window-level child, not a separate transfection. The source ASEmashr_inputsites table has an unlabeled R row-name column, which was removed. Its 1,359 coordinate IDs are shared between the methylated and unmethylated ASE result sets and are suitable for cross-condition modeling, but they do not include allele letters or rsIDs. Those identifiers would require the omitted 737-MB Joint_genotyping.vcf; no allele names were fabricated. The published ASE_mashr_results file contains only the 783 strong-ASE rows used for the reported MD/not_MD calls, so 576 other source-qualified sites are retained with explicit not_in_published_mashr_output status. The broader paper headline of 8,020 genetic-effect sites also includes monoallelic/nearly monoallelic sites that are not part of this 1,359-row cross-condition table.