The study screened 204 accessible-chromatin developmental CREs from 23 loci, together with promoter controls, in mouse embryoid bodies. This table contains aggregate scQer activity and specificity with tested mm10 coordinates and cognate ATAC annotations where available.
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
Embryoid body differentiation, day 21 endpoint
CRE libraries were integrated into mouse embryonic stem cells using piggyBac at high multiplicity, followed by embryoid-body differentiation. scQers use circular Pol III oBC detection and Pol II mBC expression to quantify activity and cell-type specificity from single-cell sequencing.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (16 of 16)
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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 · 16 definitions
element_id
CRE identifier normalized to locus:peak form.
element_class
Source element class, typically devCRE or promoter.
activity_max_cluster
Mean reporter activity in the cluster with the highest activity.
activity_all_cells
Mean reporter activity across all profiled cells.
specificity_fold_change
Specificity fold change between the maximal cluster and all cells.
active_all_replicates
Author flag for activity detected in all biological replicates.
specific_all_replicates
Author flag for specificity detected in all biological replicates.
atac_log2fc_cognate
Log2 fold change of cognate ATAC accessibility from the source data.
cognate_atac_accessibility
Cognate ATAC accessibility signal from the source data.
category
Author category for combined activity/specificity calls.
chromosome
mm10 chromosome of the tested CRE.
start_tested
Start coordinate of the PCR-tested CRE interval in mm10.
end_tested
End coordinate of the PCR-tested CRE interval in mm10.
tested_library_barcode_count
Number of final oBC-mBC pairs associated with the tested CRE.
qc_pass
TRUE for rows passing the finite-value QC filter.
source_table
Supplementary source tables used to create the row.
Quality control
The paper required valid oBC-CRE-mBC mappings and sufficient barcode-pair representation; five attempted elements without sufficient final representation were not quantified. The aggregate source table was retained for all 204 developmental CREs and five promoter controls after filtering for finite activity and specificity values.
Curation notes
The scQer aggregate table is an author-provided activity summary rather than a re-analysis of the large single-cell RDS object. The raw GSE217686 count matrices and the v2 GSE245189 matrices are retained in raw_data/geo.