Experiment / E71C7Q0M3Deep Mutational Scanning MPRA (DMS-MPRA)

5′ MPRA saturation mutagenesis of 300 bp developmental CRE tiles in PYS-2 cells

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

Five 300 bp developmental CRE tiles were assayed with all possible single-base substitutions; low-rate PCR mutagenesis also yielded single-base deletions and multi-hit molecules.

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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: CVCL:3776
Reference genome: mm39
Design focus: Variant-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. Variant effects use all barcodes associated with the focal mutation, including molecules with additional PCR-induced mutations.

Processed data

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

Visible columns (35 of 35)

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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 · 35 definitions

element_id: Parent CRE plus mutation identifier.
parent_cre: One of five 300 bp CREs.
source_class: Saturation-mutagenesis class.
sequence: Reconstructed tested WT/substitution/deletion sequence using the source-position-minus-one mapping.
sequence_length: Tested sequence length.
chromosome: Starting-tile mm39 chromosome.
start: Starting-tile 0-based mm39 start.
end: Starting-tile 0-based mm39 end.
genomic_strand: Starting-tile strand.
orientation: Not applicable.
mutation_id: Deposited mutation label.
mutation_class: WT, Mismatch, or Deletion.
ref_base: Starting-sequence base at sequence_position_1based.
alt_base: Substitution base reported in the source activity table; blank for deletions and WT.
wt_activity_mean: Mean WT activity for parent CRE.
effect_vs_wt_log2fc: Mean matched-replicate log2 variant/WT activity.
effect_vs_wt_activity_delta: Variant mean minus WT mean activity.
tile_size_bp: Tested sequence length.
tile_shift_bp: Not applicable.
activity_mean: Mean normalized activity across retained replicates.
activity_sd: Sample SD.
replicate_ids: Retained replicate labels.
n_replicates: Number of retained replicates.
n_BC_min: Minimum barcode support.
n_BC_sum: Sum of support.
log2_activity_vs_minP: Blank because source table has no minP rows.
activity_rep1a: Processed saturation-mutagenesis MPRA field.
activity_rep1b: Processed saturation-mutagenesis MPRA field.
activity_rep2a: Processed saturation-mutagenesis MPRA field.
activity_rep2b: Processed saturation-mutagenesis MPRA field.
activity_rep3a: Processed saturation-mutagenesis MPRA field.
activity_rep3b: Processed saturation-mutagenesis MPRA field.
qc_pass: 1 for constructs passing package QC.
mutation_position_source: Mutation position as reported by the source activity table (2–301).
sequence_position_1based: Actual 1-based position within the 300 bp starting sequence (source position minus 1).

Quality control

The authors reported >100 barcodes for 99.9% of substitutions, >0.65 log-activity replicate R², and marked variants with <5 barcodes as unsupported. Package QC retained finite non-negative estimates with >=5 barcodes in >=3 of 6 replicates.

Curation notes

The deposited mutation labels use source positions 2–301, which map to sequence positions 1–300 (source position minus one); this package preserves both fields. The table is mutation-level and can include additional PCR-induced mutations.

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