Targeted Methyl-STARR-seq in human SW480 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.
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Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0546
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 as (RNA + 1)/DNA 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.
methylated_enhancer_score
Enhancer activity score for the M.SssI-treated/methylated plasmid library.
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 3588/3588 rows from the Table S4 SW480 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; no rows were removed.
Curation notes
Table S4 is a significant-result table rather than the complete >134,000-CpG library count matrix. SW480 is a primary colorectal cancer cell line and is paired with metastatic SW620 in this study; source element labels include generic hg19 windows and CpG-probe-labelled windows.