Experiment / E17VM4BENSynthetic Regulatory Grammar MPRA

5′ MPRA enhancer derivatization in PYS-2 cells

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

Five 300 bp endogenous enhancers were transformed by TFBS-anchor reconstitution, randomized TFBS deposition, background/dinucleotide shuffling, and synthetic thripsis, then tested in PYS-2 cells.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CVCL:3776
Reference genome: mm39
Design focus: Synthetic / Motif-focused
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. Derivatives retained Gata4/6, Sox17, Foxa2, and Klf4 anchor units while changing backgrounds, positions, or fragment order.

Processed data

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

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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 · 32 definitions

element_id: Derivative/control identifier.
parent_cre: Source enhancer for derivative; blank for background-only controls.
source_class: Detailed transformation class.
sequence: Tested synthetic sequence.
sequence_length: Sequence length.
chromosome: Blank for synthetic constructs.
start: Blank for synthetic constructs.
end: Blank for synthetic constructs.
genomic_strand: Blank for synthetic constructs.
orientation: Not applicable.
derivative_class: Reconstitution, deposition, thripsis, background, or original class.
background_id: Background sequence identifier.
random_id: Deposition identifier.
wt_activity_mean: Matched original-sequence mean activity when available.
activity_vs_parent_log2fc: Matched-replicate log2 derivative/original activity.
activity_vs_parent_delta: Derivative mean minus original mean activity.
tile_size_bp: Construct 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_1a: Processed enhancer-derivatization MPRA field.
activity_1b: Processed enhancer-derivatization MPRA field.
activity_2a: Processed enhancer-derivatization MPRA field.
activity_2b: Processed enhancer-derivatization MPRA field.
activity_3a: Processed enhancer-derivatization MPRA field.
activity_3b: Processed enhancer-derivatization MPRA field.
qc_pass: 1 for constructs passing package QC.

Quality control

The authors reported >=0.94 log-activity replicate R², 18,405 designed constructs, and median 91 barcodes per construct. Package QC retained finite non-negative values with >=5 barcodes in >=3 of 6 replicates.

Curation notes

The sequence metadata contains 18,405 designs. The paired source activity table also contains 3,934 random_deposition_all_bkg records from a naming revision not present in the cited Zenodo sequence-metadata file; those records retain parsed parent/design/background IDs and activity but have blank sequence annotations. Other sequence joins use exact CRE_id.

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