Experiment / E7CGOV0M8Silencer / Repressor MPRA

Whole-genome RE1 MPRAduo screen in HepG2

Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay

The whole-genome RE1 library paired 200-bp human REST-binding-site sequences and controls with five benchmark E elements in HepG2. The ES plasmid library was assayed with four biological replicates and normalized to plasmid DNA.

Download processed table (CSV)Raw source data API documentation

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:0027
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal MPRAduo placed each REST/RE1 sequence in an ES duo construct with one of En02, En09, En11, En19, or En21 upstream of a GFP minimal-promoter reporter. The table joins GEO RNA/DNA replicate counts to the authors' derived per-construct DESeq-style results and emVAR allelic-skew fields.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (34 of 34)

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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 · 34 definitions

element_id: Unique source construct identifier; allele-specific constructs and enhancer/silencer pairs are encoded here.
enhancer_id: Benchmark activating element paired with the RE1 sequence.
silencer_id: Tested RE1, control, scrambled, or variant silencer identifier.
variant_id: Source variant identifier/coordinate when the silencer is allele-specific; blank for nonvariant constructs.
chromosome: Chromosome for the tested locus, from the authors' derived results.
position: Variant or locus position from the authors' derived results.
ref_allele: Reference allele for an allele-specific construct.
alt_allele: Alternate allele for an allele-specific construct.
tested_allele: Allele represented by the construct, typically ref or alt.
orientation: Sequence orientation reported by the authors, typically fwd.
variant_window: Position/window annotation within the 200-bp construct for a variant.
project: Source library annotation, such as motif, rare, maf1, scrambled, SNP, noMotif, or control.
haplotype: Haplotype annotation from the authors' derived result table.
rna_count_1: GFP cDNA barcode count in biological replicate 1.
rna_count_2: GFP cDNA barcode count in biological replicate 2.
rna_count_3: GFP cDNA barcode count in biological replicate 3.
rna_count_4: GFP cDNA barcode count in biological replicate 4.
dna_count_1: Plasmid DNA barcode count in biological replicate 1.
dna_count_2: Plasmid DNA barcode count in biological replicate 2.
dna_count_3: Plasmid DNA barcode count in biological replicate 3.
dna_count_4: Plasmid DNA barcode count in biological replicate 4.
dna_barcode_count: Observed plasmid barcode support for the oligo (source PlasmidsBCsum).
dna_count_mean: Mean plasmid DNA count across the four replicates (source plmean).
control_mean: Authors' derived mean normalized expression for the control/reference comparison.
experimental_mean: Authors' derived mean normalized expression for the tested construct.
log2_fold_change: Authors' derived log2 reporter activity estimate.
log2_fold_change_se: Standard error of the derived log2 reporter activity estimate.
test_statistic: Authors' statistical test statistic for the reporter activity comparison.
p_value: Authors' nominal p-value for the reporter activity comparison.
adjusted_p_value: Authors' Benjamini-Hochberg adjusted p-value.
allelic_log_skew: Authors' emVAR allelic-skew statistic for a matched allele comparison; blank when not applicable.
allelic_skew_log_p: Source transformed p-value for the allelic-skew test.
allelic_skew_log_fdr: Source transformed FDR for the allelic-skew test.
max_allele_frequency: Maximum population allele frequency reported by the authors' emVAR table.

Quality control

The authors required at least 10 observed plasmid barcodes per oligo and a mean plasmid DNA count of at least 20 across four replicates. This package applied those thresholds and required nonmissing log2 fold-change and standard error, retaining 123,097 of 139,325 source constructs; rows without assay output were excluded.

Curation notes

GEO accession GSM5861612 supplies the HepG2 count table. The source contains 139,325 construct rows across five E elements and multiple RE1/control classes; the processed table contains the 123,097 rows passing the stated count/effect QC. emVAR columns are blank for constructs without an allelic-skew result, which is expected for nonvariant and unsupported comparisons.

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