Experiment / E189LXZJRStandard STARR-seq

Multiplexed mSTARR-seq 400-bp regulatory-window activity

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

Genomic DNA fragments from 25 diverse 1000 Genomes individuals were multiplexed into a self-transcribing reporter library and tested in K562 cells after either M.SssI-induced methylation or mock/sham treatment. The table combines the authors' methylated and unmethylated activity models, mashr methylation-dependence results, and raw-count coverage summaries for every coverage-qualified 400-bp window.

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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:0004
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

M.SssI-induced CpG methylation versus water/mock (sham) treatment

This is the methylation-sensitive mSTARR-seq adaptation of STARR-seq. MspI-digested human genomic DNA fragments (size-selected at approximately 300–700 bp) from LCL DNA of 25 1000 Genomes individuals were given individual-specific CpG-free multiplexing barcodes and cloned into an mSTARR plasmid in which the insert is transcribed in the reporter 3′ UTR. Two independently prepared pools were each split into M.SssI-treated and mock/sham-treated plasmid libraries and transfected into K562 cells. The paper describes three methylated and three unmethylated transfections per pool and 48 h incubation; the released matrix contains 11 RNA and 11 DNA library columns labeled RNA1–RNA12 and DNA1–DNA12 with the number 11 absent.

Processed data

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Visible columns (30 of 30)

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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

window_id: Source identifier for a nonoverlapping 400-bp genomic window, formatted as chromosome_start_end.
chromosome: Chromosome parsed from window_id.
window_start_hg38: Window start coordinate parsed from the source window ID in the GRCh38/hg38 coordinate system.
window_end_hg38: Window end coordinate parsed from the source window ID in the GRCh38/hg38 coordinate system.
window_width_bp: Window width in base pairs, derived as window_end_hg38 minus window_start_hg38.
methylated_activity_beta: Source limma beta for the DNA-versus-RNA sample-type effect in the methylated condition; positive values indicate higher normalized RNA than DNA.
methylated_activity_se: Standard error of the methylated-condition activity beta.
methylated_activity_pvalue: Raw P-value for the methylated-condition DNA-versus-RNA activity test.
methylated_activity_q: Source FDR-adjusted P-value for the methylated-condition activity test.
methylated_activity_status: Authors' methylated-condition activity call: regulatory or not_regulatory.
unmethylated_activity_beta: Source limma beta for the DNA-versus-RNA sample-type effect in the unmethylated condition; positive values indicate higher normalized RNA than DNA.
unmethylated_activity_se: Standard error of the unmethylated-condition activity beta.
unmethylated_activity_pvalue: Raw P-value for the unmethylated-condition DNA-versus-RNA activity test.
unmethylated_activity_q: Source FDR-adjusted P-value for the unmethylated-condition activity test.
unmethylated_activity_status: Authors' unmethylated-condition activity call: regulatory or not_regulatory.
methylated_rna_mean_count: Arithmetic mean of raw reporter-RNA counts across the five released methylated RNA columns.
methylated_rna_detected_replicates: Number of released methylated RNA columns with a raw count greater than zero.
methylated_dna_mean_count: Arithmetic mean of raw plasmid-DNA counts across the five released methylated DNA columns.
methylated_dna_detected_replicates: Number of released methylated DNA columns with a raw count greater than zero.
unmethylated_rna_mean_count: Arithmetic mean of raw reporter-RNA counts across the six released unmethylated RNA columns.
unmethylated_rna_detected_replicates: Number of released unmethylated RNA columns with a raw count greater than zero.
unmethylated_dna_mean_count: Arithmetic mean of raw plasmid-DNA counts across the six released unmethylated DNA columns.
unmethylated_dna_detected_replicates: Number of released unmethylated DNA columns with a raw count greater than zero.
mashr_methylated_effect: mashr posterior mean for the methylated-condition regulatory activity effect, present for the 6,957 windows entered into the source mashr analysis.
mashr_unmethylated_effect: mashr posterior mean for the unmethylated-condition regulatory activity effect.
mashr_methylated_lfsr: mashr local false sign rate for the methylated-condition posterior effect.
mashr_unmethylated_lfsr: mashr local false sign rate for the unmethylated-condition posterior effect.
methylation_log2_fc: Source mashr log2 contrast between unmethylated and methylated regulatory activity.
methylation_dependency_status: Source model2 mashr call: MD or not_MD for the 6,957 tested regulatory windows; not_tested_nonregulatory for other coverage-qualified windows.
coverage_qc_passed: Boolean indicating that the window was retained by the authors' DNA/RNA coverage filter; true for every row in this table.

Quality control

The authors combined uniquely mapped reads within each replicate and used nonoverlapping 400-bp windows. A window entered the released count matrix only if it had at least one DNA read in half of the replicates from both conditions and at least one RNA read in half of the replicates in either condition, yielding 525,074 coverage-qualified windows. Activity was modeled separately by limma after voomWithQualityWeights normalization, with DNA versus RNA as the predictor and pool as a covariate; regulatory activity required positive RNA-over-DNA effect and FDR <0.01. mashr was then applied to the 6,957 windows regulatory in at least one condition plus 20,000 random null windows; the source MD/not_MD calls are retained. The package retains all 525,074 source-QC-passing windows, including biologically non-regulatory windows, and applies no additional exclusion.

Curation notes

This child table and the variant-level child table derive from the same paired mSTARR-seq transfection series. The assay is MspI-enriched genomic-fragment STARR-seq rather than an unbiased whole-genome STARR-seq experiment, so region_of_interest is null. The released model1 files omit the window ID from their header; the ID was recovered from the first field of each row. The count matrix is already coverage-filtered, so non-regulatory rows are valid tested background rather than failed QC. The paper reports 12 total transfection replicates, while the released matrix and replicateinfo file expose 11 RNA and 11 DNA columns; this release-level discrepancy is retained as an annotation rather than repaired by inventing missing columns.

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