Experiment / E6UKAQ3A8Episomal Plasmid MPRA

455-construct MPRA in HepG2 (bulk)

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

Variant-focused 455-library MPRA testing wild-type and engineered enhancer constructs in HepG2 cells. This table summarizes three paired HepG2 cDNA/plasmid samples at 48 h.

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: mm10
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Lipofectamine 3000 plasmid transfection; cDNA/plasmid harvested 48 h post-transfection

pSA293-CHEQseq episomal reporter with SCP1 promoter, chimeric intron, Venus reporter, and 11-bp barcodes for the 455 library. Counts are assigned from the Illumina/ONT barcode readouts and represented as normalized cDNA/plasmid scores.

Processed data

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Visible columns (36 of 36)

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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 · 36 definitions

element_id: Unique 455 library enhancer/variant identifier.
parent_region: Parent enhancer region or construct name.
gene: Gene associated with the parent enhancer.
mutation: Original mutation label.
mutation_edited: Normalized mutation label in the source table.
pattern: Construct pattern/category reported by the study.
window: Variant window or coordinate label.
n_mutations: Number of mutations in the construct.
sequence: Full tested reporter sequence from Supplementary Table 3.
deepliver_active_score: DeepLiver predicted activity score for the active state.
deepliver_inactive_score: DeepLiver predicted activity score for the inactive state.
deepliver_general_score: DeepLiver predicted general hepatocyte score.
deepliver_pericentral_score: DeepLiver predicted pericentral score.
deepliver_periportal_score: DeepLiver predicted periportal score.
shift_wt_deepliver_active: DeepLiver score shift from wild type for active state.
shift_wt_deepliver_inactive: DeepLiver score shift from wild type for inactive state.
shift_wt_deepliver_general: DeepLiver score shift from wild type for general state.
shift_wt_deepliver_pericentral: DeepLiver score shift from wild type for pericentral state.
shift_wt_deepliver_periportal: DeepLiver score shift from wild type for periportal state.
rna_count_total: Sum of cDNA counts across condition replicates.
dna_count_total: Sum of plasmid DNA counts across the three bulk reference plasmids.
n_rna_replicates: Number of cDNA replicates used.
n_dna_reference_replicates: Number of bulk plasmid DNA reference libraries used.
replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for bulk replicate 1.
replicate_log2_ratio_2: Library-size-normalized log2 RNA/DNA score for bulk replicate 2.
replicate_log2_ratio_3: Library-size-normalized log2 RNA/DNA score for bulk replicate 3.
replicate_log2_ratio_4: Library-size-normalized log2 RNA/DNA score for bulk replicate 4.
replicate_log2_ratio_5: Library-size-normalized log2 RNA/DNA score for bulk replicate 5.
replicate_log2_ratio_6: Library-size-normalized log2 RNA/DNA score for bulk replicate 6.
replicate_log2_ratio_7: Library-size-normalized log2 RNA/DNA score for bulk replicate 7.
replicate_log2_ratio_8: Library-size-normalized log2 RNA/DNA score for bulk replicate 8.
count_based_mean_log2_ratio: Mean of the count-derived bulk replicate scores.
count_based_median_log2_ratio: Median of the count-derived bulk replicate scores.
count_based_sd_log2_ratio: Sample standard deviation of the count-derived bulk scores.
author_condition_log2_fc: Author-reported condition log2 fold-change from Supplementary Table 3.
author_condition_padj: Author-reported BH-adjusted p-value from Supplementary Table 3.

Quality control

Author QC modeled shuffled controls with a Gaussian fit and used BH-adjusted p-values; the source description reports the same fastp Phred >30 assigned-count filtering and DESeq2 cDNA/plasmid testing. For this package, retained elements present in Supplementary Table 3 with aggregate cDNA and plasmid counts >=10 and at least two nonzero cDNA replicates. Mouse bulk scores use the three bulk plasmid references and the median reference-normalized score per cDNA replicate; all derived scores use a 0.5 pseudocount and library-size normalization.

Curation notes

Source: GSE218470 bulk 455 MPRA matrices plus Supplementary Table 3. The count matrix contains 418 constructs while the annotation table contains 455 constructs; 37 annotation-only rows were not inventively imputed and are therefore absent. The table preserves sequence, mutation, DeepLiver and author effect fields alongside count-derived scores.

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