HCT116 colorectal cancer cell metabolite lentiMPRA
Interactions Between Dietary Metabolites and Regulatory Risk Variants for Human Colon CancerA soft/random-barcoded lentiviral MPRA library tested 3,703 CRC-associated variants in 200-bp GRCh38 contexts in forward and reverse-complement orientations, alongside enhancer and transcription-factor motif controls. HCT116 cells were exposed to sodium butyrate or DCA for 6 or 24 h with vehicle controls, and the released table reports orientation-specific variant allelic, treatment, and interaction effects.
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
Vehicle control; sodium butyrate (2–5 mM) for 6 or 24 h; deoxycholic acid (100–200 uM) for 6 or 24 h.
Lentiviral delivery used a soft/random 15-bp barcode design. Barcode-to-oligo mapping used FLASH and STAR, ambiguous oligo assignments were removed, MPRAflow generated DNA/RNA barcode counts, and MPRAnalyze provided DNA-normalized likelihood-ratio-test effects. The library also included positive-control enhancer windows, TF-motif repeats/mutants, and scrambled negative controls, although the released S5 result sheet contains variant rows only.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (77 of 77)
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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 · 77 definitions
- variant_id
- dbSNP rsID for the tested variant; the source _for/_rev suffix is stored separately in orientation.
- orientation
- Construct orientation: forward or reverse_complement.
- chromosome
- GRCh38 chromosome from Supplementary Data S3.
- position_grch38
- 1-based GRCh38 position from Supplementary Data S3.
- variant_coord_grch38
- GRCh38 coordinate string from Supplementary Data S3.
- ref_allele
- Reference allele used in the library annotation; semicolon-separated when S3 contains multiple records.
- alt_allele
- Alternate allele used in the library annotation; semicolon-separated when S3 contains multiple records.
- index_snp
- CRC GWAS index SNP or SNPs linked to this tested variant in S3.
- tested_in_mpra
- MPRA library membership reported in S3.
- transcript_annotation
- S3 transcript-context annotation, such as intron, promoter, coding, or intergenic.
- epigenome_annotation
- Semicolon-separated epigenomic peak annotations used for library selection in S3.
- source_sheet
- Supplementary workbook result sheet used to populate the row.
- source_row
- 1-based row number in the source worksheet.
- allelic_logfc_alt_vs_ref
- Baseline alternate-versus-reference fragment activity effect size for this orientation (authors' logFC).
- allelic_se
- Standard error of the baseline alternate-versus-reference effect.
- allelic_pvalue
- P-value for the baseline allele effect.
- allelic_fdr
- FDR for the baseline allele effect.
- butyrate_treatment_pvalue_ref
- Overall butyrate-versus-vehicle treatment p-value for the reference construct across the experiment's treatment series.
- butyrate_treatment_pvalue_alt
- Overall butyrate-versus-vehicle treatment p-value for the alternate construct across the experiment's treatment series.
- butyrate_treatment_fdr_ref
- FDR for the overall butyrate treatment effect on the reference construct.
- butyrate_treatment_fdr_alt
- FDR for the overall butyrate treatment effect on the alternate construct.
- butyrate_6h_treatment_logfc_ref
- Butyrate-versus-vehicle treatment logFC for the reference construct at 6 h.
- butyrate_6h_treatment_logfc_alt
- Butyrate-versus-vehicle treatment logFC for the alternate construct at 6 h.
- butyrate_6h_treatment_se_ref
- Standard error of the 6-h butyrate treatment logFC for the reference construct.
- butyrate_6h_treatment_se_alt
- Standard error of the 6-h butyrate treatment logFC for the alternate construct.
- butyrate_6h_treatment_pvalue_ref
- P-value for the 6-h butyrate treatment effect on the reference construct.
- butyrate_6h_treatment_pvalue_alt
- P-value for the 6-h butyrate treatment effect on the alternate construct.
- butyrate_6h_treatment_fdr_ref
- FDR for the 6-h butyrate treatment effect on the reference construct.
- butyrate_6h_treatment_fdr_alt
- FDR for the 6-h butyrate treatment effect on the alternate construct.
- butyrate_24h_treatment_logfc_ref
- Butyrate-versus-vehicle treatment logFC for the reference construct at 24 h.
- butyrate_24h_treatment_logfc_alt
- Butyrate-versus-vehicle treatment logFC for the alternate construct at 24 h.
- butyrate_24h_treatment_se_ref
- Standard error of the 24-h butyrate treatment logFC for the reference construct.
- butyrate_24h_treatment_se_alt
- Standard error of the 24-h butyrate treatment logFC for the alternate construct.
- butyrate_24h_treatment_pvalue_ref
- P-value for the 24-h butyrate treatment effect on the reference construct.
- butyrate_24h_treatment_pvalue_alt
- P-value for the 24-h butyrate treatment effect on the alternate construct.
- butyrate_24h_treatment_fdr_ref
- FDR for the 24-h butyrate treatment effect on the reference construct.
- butyrate_24h_treatment_fdr_alt
- FDR for the 24-h butyrate treatment effect on the alternate construct.
- dca_treatment_pvalue_ref
- Overall DCA-versus-vehicle treatment p-value for the reference construct across the experiment's treatment series.
- dca_treatment_pvalue_alt
- Overall DCA-versus-vehicle treatment p-value for the alternate construct across the experiment's treatment series.
- dca_treatment_fdr_ref
- FDR for the overall DCA treatment effect on the reference construct.
- dca_treatment_fdr_alt
- FDR for the overall DCA treatment effect on the alternate construct.
- dca_6h_treatment_logfc_ref
- DCA-versus-vehicle treatment logFC for the reference construct at 6 h.
- dca_6h_treatment_logfc_alt
- DCA-versus-vehicle treatment logFC for the alternate construct at 6 h.
- dca_6h_treatment_se_ref
- Standard error of the 6-h DCA treatment logFC for the reference construct.
- dca_6h_treatment_se_alt
- Standard error of the 6-h DCA treatment logFC for the alternate construct.
- dca_6h_treatment_pvalue_ref
- P-value for the 6-h DCA treatment effect on the reference construct.
- dca_6h_treatment_pvalue_alt
- P-value for the 6-h DCA treatment effect on the alternate construct.
- dca_6h_treatment_fdr_ref
- FDR for the 6-h DCA treatment effect on the reference construct.
- dca_6h_treatment_fdr_alt
- FDR for the 6-h DCA treatment effect on the alternate construct.
- dca_24h_treatment_logfc_ref
- DCA-versus-vehicle treatment logFC for the reference construct at 24 h.
- dca_24h_treatment_logfc_alt
- DCA-versus-vehicle treatment logFC for the alternate construct at 24 h.
- dca_24h_treatment_se_ref
- Standard error of the 24-h DCA treatment logFC for the reference construct.
- dca_24h_treatment_se_alt
- Standard error of the 24-h DCA treatment logFC for the alternate construct.
- dca_24h_treatment_pvalue_ref
- P-value for the 24-h DCA treatment effect on the reference construct.
- dca_24h_treatment_pvalue_alt
- P-value for the 24-h DCA treatment effect on the alternate construct.
- dca_24h_treatment_fdr_ref
- FDR for the 24-h DCA treatment effect on the reference construct.
- dca_24h_treatment_fdr_alt
- FDR for the 24-h DCA treatment effect on the alternate construct.
- butyrate_allele_interaction_pvalue
- Overall p-value for the butyrate × allele interaction, i.e. change in the alternate-versus-reference effect under butyrate.
- butyrate_allele_interaction_fdr
- FDR for the overall butyrate × allele interaction.
- butyrate_6h_allele_interaction_logfc_alt_vs_ref
- Change in the alternate-versus-reference activity effect under butyrate at 6 h (interaction logFC).
- butyrate_6h_allele_interaction_se
- Standard error of the 6-h butyrate × allele interaction logFC.
- butyrate_6h_allele_interaction_pvalue
- P-value for the 6-h butyrate × allele interaction.
- butyrate_6h_allele_interaction_fdr
- FDR for the 6-h butyrate × allele interaction.
- butyrate_24h_allele_interaction_logfc_alt_vs_ref
- Change in the alternate-versus-reference activity effect under butyrate at 24 h (interaction logFC).
- butyrate_24h_allele_interaction_se
- Standard error of the 24-h butyrate × allele interaction logFC.
- butyrate_24h_allele_interaction_pvalue
- P-value for the 24-h butyrate × allele interaction.
- butyrate_24h_allele_interaction_fdr
- FDR for the 24-h butyrate × allele interaction.
- dca_allele_interaction_pvalue
- Overall p-value for the DCA × allele interaction, i.e. change in the alternate-versus-reference effect under DCA.
- dca_allele_interaction_fdr
- FDR for the overall DCA × allele interaction.
- dca_6h_allele_interaction_logfc_alt_vs_ref
- Change in the alternate-versus-reference activity effect under DCA at 6 h (interaction logFC).
- dca_6h_allele_interaction_se
- Standard error of the 6-h DCA × allele interaction logFC.
- dca_6h_allele_interaction_pvalue
- P-value for the 6-h DCA × allele interaction.
- dca_6h_allele_interaction_fdr
- FDR for the 6-h DCA × allele interaction.
- dca_24h_allele_interaction_logfc_alt_vs_ref
- Change in the alternate-versus-reference activity effect under DCA at 24 h (interaction logFC).
- dca_24h_allele_interaction_se
- Standard error of the 24-h DCA × allele interaction logFC.
- dca_24h_allele_interaction_pvalue
- P-value for the 24-h DCA × allele interaction.
- dca_24h_allele_interaction_fdr
- FDR for the 24-h DCA × allele interaction.
Quality control
Study QC retained uniquely mapped barcode-oligo pairs with alignment quality >=100, removed sequences detected on multiple oligos, and selected a random set of 50 barcodes per fragment when the summed plasmid-DNA counts for replicates 1 and 2 exceeded 10; final effects were calculated by MPRAnalyze after DNA normalization. The released S5 result rows were retained only when an orientation-qualified variant ID, S3 annotation join, and result row were valid; 7,323 of 7,323 released rows passed these package-level checks and no rows were removed. Numeric NA values are represented as blank cells in the processed CSV.
Curation notes
Supplementary Data S5 contains 7,323 orientation-specific variant rows representing 3,691 distinct rsIDs; 3,632 variants have both orientations and 59 have only one released orientation. This is below the 3,703-variant design count described in the paper, so omitted variants were not imputed. The result sheet does not include the library's enhancer, TF-motif, or scramble control elements. S3 records duplicated across multiple GWAS index SNPs were collapsed into semicolon-separated unique annotation values, and source numeric NA values were converted to blanks.