Experiment / E59NC7AJ2Episomal Plasmid MPRA

5′ MPRA model-guided enhancer compaction in PYS-2 cells

Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers

ChromBPNet-guided iterative single-base deletions generated trajectories from five 300 bp endogenous enhancer tiles toward 40 bp; synthesized compacted sequences were tested by MPRA in PYS-2 cells.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CVCL:3776
Reference genome: mm39
Design focus: Other
Region of interest: chr4:111340574-111340874,chr11:55319627-55319927,chr14:63468603-63468903,chr17:67961106-67961406,chr17:87048616-87048916

Perturbation & assay details

Basal / Untreated

5′ episomal plasmid MPRA using the p001-PB-MPRA/minP reporter with a degenerate barcode in the reporter 5′ UTR; RNA and DNA barcode UMIs were sequenced separately and activity was quantified as a normalized 1% Winsorized RNA/DNA ratio. Length-stratified end-to-end mapping prevented short constructs from spuriously mapping to longer constructs; 40–45 bp constructs were lost during size selection.

Processed data

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

Visible columns (28 of 28)

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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 · 28 definitions

element_id: Compacted construct or control identifier.
parent_cre: Parent 300 bp CRE.
source_class: Deposited class.
sequence: Tested compacted/reference sequence when available.
sequence_length: Sequence length.
chromosome: Parent mm39 chromosome when available.
start: Parent-tile 0-based mm39 start when available.
end: Parent-tile 0-based mm39 end when available.
genomic_strand: Parent sequence strand.
orientation: Not applicable.
deletion_id: Model-selected deleted base identifier.
deletion_count: Cumulative deleted bases.
compacted_length: Construct length.
activity_vs_parent_log2fc: Matched-replicate log2 compacted/parent activity.
activity_vs_parent_delta: Compacted mean minus parent mean activity.
tile_size_bp: Compacted sequence length.
tile_shift_bp: Not applicable.
activity_mean: Mean normalized activity.
activity_sd: Sample SD.
replicate_ids: Retained replicate labels.
n_replicates: Number of retained replicates.
n_BC_min: Minimum support.
n_BC_sum: Sum support.
log2_activity_vs_minP: Mean log2 activity relative to minP.
activity_1: Processed compaction MPRA field.
activity_2: Processed compaction MPRA field.
activity_3: Processed compaction MPRA field.
qc_pass: 1 for constructs passing package QC.

Quality control

The authors reported >0.98 log-activity replicate R² and length-stratified mapping. Package QC retained finite non-negative activity values with >=5 barcodes in all >=3 biological replicates.

Curation notes

The source includes 1,253 compact constructs from the five model CREs plus full/reference and promoter controls. Parent coordinates and strand in the processed table come from the deposited 300 bp starting-tile metadata; compact construct sequences themselves are retained from the compaction metadata.

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