Experiment / E80X4M2XUTransposon-integrated MPRA

Bulk MPRA reporter architecture controls during mEB differentiation

Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters

Pooled piggyBac reporter libraries varied U6/oBC presence, CRE position, promoter configuration and reporter architecture during mouse embryoid-body differentiation. The table contains construct-level winsorized RNA/DNA activity across days 0, 4, 18, 20 and 22.

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: UNMAPPED:mouse_embryoid_body
Reference genome: mm10
Design focus: Other
Region of interest: Not reported / not applicable

Perturbation & assay details

mEB differentiation time course, days 0-22

Reporter architecture libraries were delivered by piggyBac into mouse embryonic stem cells and measured by bulk MPRA. The source activity is based on 1% winsorized DNA and RNA UMI sums and includes upstream/downstream CRE placement, no-promoter, no-oBC and promoter-control constructs.

Processed data

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

Visible columns (20 of 20)

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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 · 20 definitions

pool_id: Bulk MPRA library pool identifier.
library_id: Originating library identifier.
reporter_architecture: Short source description of the reporter architecture.
cre_position: Position of the CRE relative to the promoter.
reporter_orf: Reporter open reading frame.
promoter: Promoter identity in the reporter construct.
u6_obc: Whether the Pol III U6/oBC cassette is present.
chs4: Whether cHS4 insulators are present.
element_class: Source element class, devCRE or promoter.
element_id: CRE or promoter identifier.
biological_replicate: Biological replicate identifier.
technical_replicate: Technical/library-preparation replicate identifier.
time_point_day: mEB harvest day.
dna_barcode_count: Number of detected DNA barcodes contributing to the construct summary.
dna_umi_sum_winsorized: 1% winsorized sum of DNA UMIs.
rna_umi_sum_winsorized: 1% winsorized sum of RNA UMIs.
activity_rna_over_dna: RNA UMI sum divided by DNA UMI sum.
reported_activity_winsorized: Activity reported in the supplementary source table.
qc_pass: TRUE for rows passing the ingestion QC filters.
source_table: Supplementary source table used to create the row.

Quality control

The source analysis used a >3 DNA-read-per-barcode inclusion threshold. For a robust construct-level table, rows were additionally required to have at least 10 detected DNA barcodes, positive DNA UMI sum, finite RNA sum and finite reported activity; 332 low-barcode rows were excluded.

Curation notes

The raw v2 pool-A and pool-B mEB matrices are retained in raw_data/geo alongside the compact author summary. The cHS4 field is TRUE for all rows in this source table; U6/oBC and CRE position distinguish the tested architectures.

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