Experiment / E9NM8NU9BEpisomal Plasmid MPRA

5′ MPRA multi-size sub-tiling v2 in PYS-2 cells

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

A dense library of 40, 70, 120, 170, 220, 270, and 300 bp tiles at 5 bp stride, in original and reverse-complement orientations, was assayed in PYS-2 cells.

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: CVCL:3776
Reference genome: mm39
Design focus: Region-focused
Region of interest: chr1:153252099-153252954,chr2:147959110-147960060,chr3:34811727-34812787,chr3:34814505-34816220,chr4:111340255-111341084,chr11:55319143-55320037,chr12:31271347-31271867,chr14:63468389-63469238,chr17:67960827-67961711,chr17:87048297-87049296

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. This library was co-transfected with the saturation-mutagenesis library.

Processed data

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

Visible columns (27 of 27)

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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 · 27 definitions

element_id: Unique tile/control identifier.
parent_cre: Original developmental CRE.
source_class: Activity-table class.
sequence: Tested tile sequence when available.
sequence_length: Sequence length in bp.
chromosome: mm39 chromosome.
start: 0-based mm39 start.
end: 0-based mm39 end.
genomic_strand: Sequence strand.
orientation: Original or reverse-complement orientation.
twist_library_id: Synthesis/library identifier.
tile_size_bp: Tile size in bp.
tile_shift_bp: Tile shift in bp.
activity_mean: Mean normalized RNA/DNA 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 barcode supports.
log2_activity_vs_minP: Mean log2 activity relative to minP.
activity_rep1a: Processed multi-size sub-tiling MPRA field.
activity_rep1b: Processed multi-size sub-tiling MPRA field.
activity_rep2a: Processed multi-size sub-tiling MPRA field.
activity_rep2b: Processed multi-size sub-tiling MPRA field.
activity_rep3a: Processed multi-size sub-tiling MPRA field.
activity_rep3b: Processed multi-size sub-tiling MPRA field.
qc_pass: 1 for constructs passing package QC.

Quality control

Author-processed activity tables already applied the DNA-UMI >=2 barcode filter and 1% Winsorization. Package QC retained finite non-negative activity entries with >=5 barcodes per replicate and >=3 QC-passing biological replicates per construct; mean and SD are across retained replicates. Final table contains 11366 constructs.

Curation notes

PYS-2 is ATCC CRL-2745 / Cellosaurus CVCL_3776. v2 and saturation mutagenesis were co-transfected but are separate child experiments because their designs differ.

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