Baseline methylated-versus-unmethylated mSTARR-seq in K562 cells
Genome-wide quantification of the effects of DNA methylation on human gene regulationA genome-scale library of GM12878 genomic fragments was cloned into the CpG-free pmSTARRseq1 self-transcribing reporter and assayed after either M.SssI methylation or mock/sham treatment. The two plasmid states were transfected into human K562 cells, and reporter RNA was compared with plasmid DNA input across the primary replicate set.
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 CpG methylation versus mock/sham treatment
Methylation-adapted episomal STARR-seq (mSTARR-seq) using the CpG-free pmSTARRseq1 vector (Addgene #96945). Randomly sheared and MspI-digested GM12878 genomic DNA was mixed at 2:1 and cloned by Gibson assembly into the reporter 3' UTR. M.SssI-treated and sham-treated plasmid pools were transfected into K562 cells with six planned replicates per condition; after 48 hours, plasmid DNA input and plasmid-derived mRNA were sequenced as 100-bp paired-end libraries. Reads were uniquely mapped to hg38 and summarized over non-overlapping 200-bp windows. The processed table retains the authors' primary baseline model statistics, including the nested RNA-versus-DNA effects in each methylation state and the methylation-by-library-type interaction where supplied.
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 · 23 definitions
- window_id
- Unique hg38 200-bp window identifier in chromosome:start-end form; coordinates retain the source interval convention.
- chromosome
- Human hg38 chromosome name.
- start_hg38
- Start coordinate of the analyzed 200-bp hg38 interval, as supplied by the article's window table.
- end_hg38
- End coordinate of the analyzed 200-bp hg38 interval, as supplied by the article's window table.
- methylated_library_type_beta
- Published nested-model beta for the library-type effect in the M.SssI-methylated condition; in the source encoding, negative values are the direction used for more reporter RNA than DNA input.
- methylated_library_type_se
- Standard error of the methylated-condition library-type beta.
- methylated_library_type_pvalue
- Published p-value for the methylated-condition library-type effect.
- methylated_library_type_fdr
- Published FDR-corrected p-value for the methylated-condition library-type effect.
- unmethylated_library_type_beta
- Published nested-model beta for the library-type effect in the mock/sham-unmethylated condition; in the source encoding, negative values are the direction used for more reporter RNA than DNA input.
- unmethylated_library_type_se
- Standard error of the unmethylated-condition library-type beta.
- unmethylated_library_type_pvalue
- Published p-value for the unmethylated-condition library-type effect.
- unmethylated_library_type_fdr
- Published FDR-corrected p-value for the unmethylated-condition library-type effect.
- methylated_activity_call
- TRUE when the methylated-condition beta is <0 and its matching FDR is <0.1; this reproduces the reported activity direction from the supplementary table.
- unmethylated_activity_call
- TRUE when the unmethylated-condition beta is <0 and its matching FDR is <0.1; this reproduces the reported activity direction from the supplementary table.
- enhancer_activity_call
- TRUE when either methylation condition passes its corresponding beta<0 and FDR<0.1 activity rule; 19,703 rows pass.
- md_interaction_beta
- Published beta for the condition-by-library-type interaction from Supplementary file 4; negative values indicate higher activity in the unmethylated state under the source encoding.
- md_interaction_se
- Standard error of the condition-by-library-type interaction beta.
- md_interaction_pvalue
- Published p-value for the condition-by-library-type interaction.
- md_interaction_fdr
- Published FDR-corrected p-value for the condition-by-library-type interaction.
- md_direction
- Direction of methylation dependence for rows with interaction output and FDR<0.1; otherwise 'No significant methylation dependence' when an interaction row exists, blank when no interaction row was supplied.
- md_activity_call
- TRUE when the supplied interaction FDR is <0.1; FALSE when an interaction row exists but does not pass that threshold; blank when Supplementary file 4 has no row for the window.
- md_model_available
- TRUE when the window has a row in the article's interaction-model Supplementary file 4.
- qc_pass
- TRUE for every row retained from the authors' 262,829-window post-QC analysis set.
Quality control
The authors trimmed adapters and low-quality bases, retained uniquely mapped reads, excluded one main-experiment replicate pair for low sequencing depth, removed windows with zero mRNA counts in three or more replicates per condition, and removed regions with unstable or poorly repeatable DNA counts (>25% of replicate pairs outside the central 90th percentile of pairwise differences). These filters left 262,829 analyzable 200-bp windows, all retained in table.csv. The paper's reported 19,703 regulatory windows are reproduced from Supplementary file 3 by calling a condition active when its library-type beta is <0 and its matching FDR is <0.1; this sign orientation agrees with the reported count and the interaction-direction results, although the narrative methods text displays the opposite beta inequality. Supplementary file 4 supplies interaction results for 17,849 of the 19,703 activity windows; missing interaction fields indicate that no row was supplied in that file, not a negative call.
Curation notes
This package represents the primary baseline mSTARR-seq experiment. The paper also generated an additional interferon-alpha challenge set (methylated IFNA+ versus methylated IFNA- plus two unmethylated controls) and deposited its sequencing libraries in SRP120556, but did not provide a structured window-level IFNA effect table among this paper's supplementary files; raw sequencing reads are intentionally not included per the ingestion scope. Low-throughput luciferase validation is not a separate MPRA experiment. The source spreadsheets are preserved in raw_data, and the generated table combines Supplementary files 3 and 4 by exact chromosome/start/end coordinates.