Experiment / E2278N1FVEpisomal Plasmid MPRA

12K accessible-region MPRA in mouse liver

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

Episomal 12K library testing 10,845 accessible mouse hepatocyte regions with shuffled negatives and positive controls after hydrodynamic delivery. This table summarizes seven paired in vivo mouse liver cDNA/plasmid samples across the 5-prime and 3-prime barcode versions.

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: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: UBERON:0002107
Reference genome: mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Hydrodynamic tail-vein delivery of 20 µg MPRA plasmid; liver harvested 24 h post-injection

pSA293-CHEQseq episomal plasmid reporter with SCP1 promoter, chimeric intron, Venus reporter, and 12-bp barcodes; cDNA/plasmid barcode counts were assigned with the study's CHEQ-seq workflow and summarized as normalized RNA/DNA scores.

Processed data

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

Visible columns (33 of 33)

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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 · 33 definitions

element_id: Unique 12K library enhancer identifier.
chromosome: Chromosome parsed from the cloned enhancer coordinate.
start: Start coordinate as reported in the source coordinate string.
end: End coordinate as reported in the source coordinate string.
enhancer_barcode: 12-bp barcode associated with the cloned enhancer.
reference_genome: Assembly reported for the source sequence, usually mm10.
mlv_enhancer_region: Broader MLV/accessible region associated with the cloned enhancer.
enhancer_type: Source annotation for the enhancer.
hepatocyte_shared_class: Hepatocyte shared chromatin class.
hepatocyte_topic_class: Hepatocyte topic class.
hepatocyte_refined_class: Refined hepatocyte class.
hepatocyte_consensus_class: Consensus hepatocyte class.
annotation: Genomic annotation such as promoter, intron, or intergenic.
distance_to_tss: Reported distance to the nearest transcription start site.
nearest_gene: Nearest or associated gene symbol.
linked_genes: Linked gene symbols reported by the study.
regulon: Regulon annotation reported by the study.
rna_count_total: Sum of RNA/cDNA counts across retained condition replicates.
dna_count_total: Sum of plasmid DNA counts across retained condition replicates.
n_replicates: Number of biological cDNA/plasmid paired samples used.
replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for condition replicate 1.
replicate_log2_ratio_2: Library-size-normalized log2 RNA/DNA score for condition replicate 2.
replicate_log2_ratio_3: Library-size-normalized log2 RNA/DNA score for condition replicate 3.
replicate_log2_ratio_4: Library-size-normalized log2 RNA/DNA score for condition replicate 4.
replicate_log2_ratio_5: Library-size-normalized log2 RNA/DNA score for condition replicate 5.
replicate_log2_ratio_6: Library-size-normalized log2 RNA/DNA score for condition replicate 6.
replicate_log2_ratio_7: Library-size-normalized log2 RNA/DNA score for condition replicate 7.
count_based_mean_log2_ratio: Mean of the count-derived replicate log2 RNA/DNA scores.
count_based_median_log2_ratio: Median of the count-derived replicate log2 RNA/DNA scores.
count_based_sd_log2_ratio: Sample standard deviation of the count-derived replicate scores.
author_condition_log2_fc: Author-reported condition log2 fold-change from Supplementary Table 2.
author_condition_padj: Author-reported BH-adjusted p-value from Supplementary Table 2.
main_12k_activity_pattern: Author 12K activity call: Both, HepG2, Invivo, or None.

Quality control

Author QC: assigned barcode counts were quality-filtered with fastp (Phred >30), modeled against shuffled negative controls with a Gaussian fit, and BH-adjusted; the paper called elements active at padj <0.1. For this package, retained only count IDs present in Supplementary Table 2 with a nonblank author activity_pattern (None, Invivo, HepG2, or Both); assignment-only columns were excluded. Count-derived scores use a 0.5 pseudocount and library-size normalization.

Curation notes

Source: GSE218471 12K MPRA count matrix plus Supplementary Table 2. The source matrix has 11,871 elements; the author table has 7,199 nonblank activity calls (the article text reports 7,198 in one figure description). The table retains the 7,199 rows called by the source table, including its 'None' inactive call. The source includes both 5-prime and 3-prime barcode versions; scores combine all available paired mouse samples for this condition.

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