Experiment / E97VTAV9CEpisomal Plasmid MPRA

5′ MPRA sub-tiling v1 in PYS-2 cells

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

A 270 bp, 5 bp-stride sub-tiling library covering ten developmental CRE intervals was assayed in PYS-2 parietal endoderm-like mouse cells.

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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,chr4:111340259-111341084,chr11:55319147-55320037,chr12:31271347-31271867,chr14:63468393-63469238,chr17:67960831-67961711,chr17:87048301-87049296

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.

Processed data

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

Visible columns (25 of 25)

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Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 25 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 retrieval strand.
orientation: Original v1 reporter orientation.
tile_size_bp: Tile size in bp.
tile_shift_bp: Tile shift within source interval in bp.
activity_mean: Mean deposited MPRA activity across QC-passing replicates.
activity_sd: Sample SD across retained replicates.
replicate_ids: Retained biological replicate labels.
n_replicates: Number of retained replicates.
n_BC_min: Minimum barcode support across retained replicates.
n_BC_sum: Sum of barcode supports.
log2_activity_vs_minP: Mean replicate-level log2(activity/minP).
activity_biol_rep1: Processed MPRA construct or summary field.
activity_biol_rep2: Processed MPRA construct or summary field.
activity_biol_rep3: Processed MPRA construct or summary field.
activity_biol_rep4: Processed MPRA construct or summary field.
activity_biol_rep6: Processed MPRA construct or summary 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 1330 constructs.

Curation notes

PYS-2 is ATCC CRL-2745 and Cellosaurus CVCL_3776; source includes ten original CREs and controls.

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