K562 mSTARR-seq baseline: methylated versus sham-treated library
DNA methylation-environment interactions in the human genomeCaptured human genomic DNA from GM12878 was cloned into the episomal pmSTARRseq1 reporter, treated with M.SssI or a sham reaction, and transfected into K562 cells. The table contains model statistics for 216,091 study-QC-passed windows under baseline/vehicle conditions.
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 (vehicle control; 6 h)
mSTARR-seq is an epigenetically manipulated episomal STARR-seq assay: approximately 600-700 bp captured genomic fragments were cloned into the 3' transcribed region of pmSTARRseq1, enzymatically methylated with M.SssI or sham-treated, transfected into K562, and quantified by paired plasmid DNA and self-transcribed RNA sequencing. Six replicate RNA/DNA libraries were generated for each methylation condition in the baseline K562 assay.
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 · 26 definitions
- element_id
- Human-readable genomic interval identifier, formatted chromosome:start-end.
- source_window_id
- Original eLife supplemental-table window identifier, formatted chromosome_start_end.
- chromosome
- Reference chromosome or contig.
- start_bp
- 0-based interval start inferred from the source window identifier.
- end_bp
- End-exclusive interval end inferred from the source window identifier.
- window_length_bp
- Interval length in base pairs; normally 600, with the terminal chrM interval reported as 369.
- methylation_condition_p
- P-value for the source model's methylation-condition coefficient.
- methylation_condition_beta
- Source model beta for the methylation-condition term.
- methylation_condition_se
- Standard error of the methylation-condition beta.
- methylated_activity_p
- P-value for RNA versus DNA activity in the methylated condition.
- methylated_activity_beta
- RNA-versus-DNA sample-type beta in the methylated condition; positive values indicate excess reporter RNA relative to input DNA.
- methylated_activity_se
- Standard error of the methylated-condition activity beta.
- methylated_activity_fdr
- Empirical FDR for methylated-condition activity; blank means the source did not report an FDR for that window.
- unmethylated_activity_p
- P-value for RNA versus DNA activity in the sham/unmethylated condition.
- unmethylated_activity_beta
- RNA-versus-DNA sample-type beta in the sham/unmethylated condition; positive values indicate excess reporter RNA relative to input DNA.
- unmethylated_activity_se
- Standard error of the unmethylated-condition activity beta.
- unmethylated_activity_fdr
- Empirical FDR for unmethylated-condition activity; blank means the source did not report an FDR for that window.
- methylation_dependence_beta
- RNA/DNA activity interaction beta comparing methylated with sham/unmethylated DNA; negative values indicate lower activity when methylated.
- methylation_dependence_se
- Standard error of the methylation-dependence interaction beta.
- methylation_dependence_t
- T statistic for the methylation-dependence interaction.
- methylation_dependence_p
- P-value for the methylation-dependence interaction.
- methylation_dependence_fdr
- Empirical FDR for methylation-dependent activity; blank means the source did not report an interaction FDR for that window.
- methylated_activity_significant
- yes when methylated_activity_beta is positive and methylated_activity_fdr < 0.01; otherwise no.
- unmethylated_activity_significant
- yes when unmethylated_activity_beta is positive and unmethylated_activity_fdr < 0.01; otherwise no.
- methylation_dependence_significant
- yes when at least one activity call is positive and methylation_dependence_fdr < 0.01; otherwise no.
- methylation_dependence_direction
- Sign of the estimated methylation-dependence beta irrespective of significance; not_tested when the source interaction beta is unavailable.
Quality control
Official study QC retained windows with nonzero DNA counts in at least 3 methylated and 3 sham DNA replicates, nonzero RNA counts in at least 3 replicates in either methylation condition, and high DNA replicate repeatability following Lea et al. 2018. For this dataset, 5,051,776 starting windows became 4,558,475 after the DNA filter, 253,501 after the RNA filter, and 216,091 after DNA repeatability filtering. The study excluded baseline sham RNA sample L31250 and its paired DNA sample before analysis because of an unusually high proportion of zero counts. The processed table retains all final source rows; activity calls require a positive RNA/DNA beta and FDR <0.01, and methylation-dependent calls additionally require interaction FDR <0.01.
Curation notes
The captured input library was made from GM12878 DNA and assayed after transfection into K562, so the biosample is K562 and the sequences are genomic windows rather than allele contrasts. The source includes one 369-bp terminal chrM interval (chrM:16200-16569); all other intervals are 600 bp, and the terminal interval was retained as a valid contig-end window. Source NA values are represented as blank cells in table.csv and indicate model terms not reported for windows without a positive RNA/DNA activity beta, not failed QC.