Targeted Methyl-STARR-seq in human HEK293T cells used 120-bp genomic fragments centered on H3K27ac summits or CRC DMR CpGs cloned into pmSTARRseq1. M.SssI-treated methylated and mock-treated unmethylated plasmid libraries were compared after transfection, with RNA collected 36 hours later.
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:0063
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; M.SssI-treated methylated versus mock-treated unmethylated plasmid libraries
The methylation library used 120-bp synthetic fragments centered on H3K27ac peak summits or CRC differential-methylation CpGs. Half of the pmSTARRseq1 plasmid library was methylated in vitro with M.SssI and the other half was mock treated; bisulfite conversion was assessed, and EAS was calculated from DESeq2-normalized RNA/DNA counts where supplied across three biological and three technical PCR replicates.
Processed data
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Column dictionary · 15 definitions
element_id
Normalized source element label with the leading '>' removed.
source_element
Source identifier prefix: hg19 for a generic enhancer-centered window, cg... for an Illumina CpG probe, or hg19pc for a human control.
methyl_cpg_locus
Original Table S4 locus label, including its leading '>' prefix.
chromosome
Human chromosome for the tested window in hg19.
window_start_hg19
Start coordinate of the reported genomic window in hg19.
window_end_hg19
End coordinate of the reported genomic window in hg19.
window_length_bp
Reported length of the tested window in base pairs, normally 120.
cpg_offset_0based
Reported zero-based offset of the tested CpG within the window.
log2_methylated_unmethylated
Source-reported log2 ratio of methylated versus unmethylated enhancer activity score.
p_value
Raw two-sided t-test P value for the methylation effect.
p_adjusted
Multiple-testing-adjusted P value from the source table.
unmethylated_enhancer_score
Enhancer activity score for the mock-treated/unmethylated plasmid library; blank because the HEK293T source worksheet does not provide this column.
methylated_enhancer_score
Enhancer activity score for the M.SssI-treated/methylated plasmid library; blank because the HEK293T source worksheet does not provide this column.
cell_line
Cell line represented by this experiment.
source_table
Supplementary workbook and worksheet of origin.
Quality control
The authors assessed bisulfite conversion, used three biological replicates and three technical PCR replicates, normalized RNA/DNA counts with DESeq2, and selected methylation-sensitive results using two-sided t tests with adjusted P < 0.05. Packaging QC retained 2470/2547 rows from the Table S4 HEK293T worksheet after requiring a human hg19/CpG-probe locus with a valid window, finite effect and probabilities in [0,1], p_adjusted < 0.05, and nonnegative enhancer scores where supplied. The 77 sacCer3 control/spike-in loci were excluded as non-human; no other rows were removed.
Curation notes
Table S4 contains a fourth, non-CRC human cell-line worksheet for HEK293T in addition to the three CRC contexts emphasized in the main text; it is retained as a separate experiment. The source worksheet also contains 77 Saccharomyces cerevisiae sacCer3 control/spike-in loci, which are retained in raw_data but omitted from the processed human table. The HEK293T worksheet has no EAS columns, so those fields remain blank rather than being imputed.