Methylation-state STARR-seq of captured glioblastoma regulatory elements in U87 cells
Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variationThe AK100 (library #100) target-enriched captured-fragment library was assayed in U87 glioblastoma cells in unmethylated and in-vitro remethylated plasmid states. Public GEO segment-count matrices were mapped to the same 500-bp, 50%-overlapping hg19 windows used for the study summary, and paired windows with observed DNA and reporter RNA in both states were retained.
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
Unmethylated plasmid library versus in-vitro CpG-remethylated plasmid library using M.SssI
This is the U87 cell-line arm of the modified episomal pGL3-promoter self-transcribing reporter assay. Captured genomic segments were cloned downstream of the minimal promoter; bacterial propagation supplied the demethylated state and M.SssI treatment supplied the matched remethylated state. U87 DNA/RNA segment counts were aggregated over the source 500-bp windows, and TAS was recalculated for each state as log2((RNA_window/DNA_window)/(RNA_total/DNA_total)).
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 · 18 definitions
- element_id
- Source Table S7 identifier for the matched 500-bp hg19 window.
- chromosome
- Chromosome name for the hg19 coordinate.
- start_hg19
- Start coordinate of the source 500-bp window in hg19.
- end_hg19
- End coordinate of the source 500-bp window in hg19.
- width_bp
- Window width in base pairs, calculated as end_hg19 - start_hg19 + 1.
- fragment_count_unmethylated
- Number of U87 source segment rows with positive RNA count contributing to the unmethylated window.
- dna_count_unmethylated
- Aggregated U87 plasmid DNA count for the unmethylated state.
- rna_count_unmethylated
- Aggregated U87 reporter RNA count for the unmethylated state.
- tas_unmethylated
- Recalculated U87 transcriptional activity score for the unmethylated state; log2 normalized RNA/DNA activity.
- fragment_count_remethylated
- Number of U87 source segment rows with positive RNA count contributing to the remethylated window.
- dna_count_remethylated
- Aggregated U87 plasmid DNA count for the in-vitro remethylated state.
- rna_count_remethylated
- Aggregated U87 reporter RNA count for the in-vitro remethylated state.
- tas_remethylated
- Recalculated U87 transcriptional activity score for the remethylated state.
- delta_tas
- Change in U87 TAS after remethylation (tas_remethylated - tas_unmethylated).
- activity_unmethylated
- Derived activity class in the unmethylated state: enhancer for TAS > 0 or silencer for TAS < 0.
- activity_remethylated
- Derived activity class in the remethylated state: enhancer for TAS > 0 or silencer for TAS < 0.
- activity_switch
- Derived yes/no flag indicating whether the TAS sign changes between methylation states.
- tas_change_direction
- Derived direction of delta_tas: increased, decreased, or unchanged.
Quality control
The public GEO matrices contain the authors' on-target mapped segment counts. Rows with no RNA count were excluded under the study's on-target inclusion rule; U87 segments were assigned to every overlapping source 500-bp window. The packaged table retains 41,716 of 42,182 source windows with positive DNA and RNA counts in both methylation states. No U87-specific per-window p-values or FDR values were provided in the public processed matrices, so this table is a descriptive paired activity table rather than a significance-filtered replication of Table S7.
Curation notes
GEO provides separate U87 matrices but the article's main Supplementary Table S7 is the T98G summary. This table was generated by joining the U87 unmethylated and remethylated matrices to the same 42,182 source windows, aggregating overlapping segment counts, normalizing each state by its U87-wide positive-RNA segment totals, and retaining paired windows with positive DNA/RNA in both states. U87-specific significance statistics were not available. The GEO record names the cell line U87; CVCL:0022 is the standard U-87MG ATCC Cellosaurus mapping, although Cellosaurus flags that line as problematic/misidentified, so the exact provenance is noted as an ambiguity.