A piggyBac-integrated library of developmental CREs and promoter controls was measured by bulk MPRA during mouse embryoid-body differentiation. The table aggregates mBC-level GSE217679 counts per CRE, replicate and time point and includes the corresponding published activity summary when it matched.
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
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
mEB differentiation time course, days 0-21
Pooled reporter constructs were delivered by piggyBac into mouse embryonic stem cells and sampled through embryoid-body differentiation. Activity is recomputed as sample-normalized RNA UMI divided by sample-normalized DNA UMI from the mBC count matrix.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (18 of 18)
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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 · 18 definitions
element_id
CRE identifier normalized to locus:peak form.
source_cre_id
CRE identifier as supplied in the GEO count matrix.
element_class
Source class of the CRE or promoter control.
biological_replicate
Bulk MPRA biological replicate identifier.
time_point_day
Embryoid-body differentiation day.
library_batch
Library preparation batch.
mBC_count_qc
Number of mBC rows passing the >20 DNA-read filter.
dna_umi_sum_qc
Sum of DNA UMIs over QC-passing mBCs.
rna_umi_sum_qc
Sum of RNA UMIs over QC-passing mBCs.
dna_read_sum_qc
Sum of DNA reads over QC-passing mBCs.
rna_read_sum_qc
Sum of RNA reads over QC-passing mBCs.
dna_umi_normalized_sum
QC-passing DNA UMI sum divided by the total DNA UMI count for the sample.
rna_umi_normalized_sum
QC-passing RNA UMI sum divided by the total RNA UMI count for the sample.
activity_raw_rna_over_dna
Recomputed normalized RNA/DNA activity score.
published_activity
Published activity value from the author-provided time-series summary, when matched.
published_mBC_count
Published number of measured mBCs for the matched CRE/sample group.
qc_pass
TRUE for rows passing the ingestion QC filters.
source_table
GEO and supplementary source tables used to create the row.
Quality control
At the mBC level, rows were required to have more than 20 DNA reads, matching the paper's bulk time-series representation filter. CRE/sample groups were retained only with at least 20 qualifying mBCs; the paper-noted low-quality day20 replicate 2B1 sample was excluded. RNA/DNA sums and normalized activity were required to be finite and nonzero.
Curation notes
The processed table deliberately removes low-coverage CRE/sample groups, while the complete compressed GSE217679 count matrix remains in raw_data/geo. Nineteen raw group keys did not have a corresponding published summary row; those raw-derived rows are retained when they pass QC.