The study used scQers in mouse embryoid bodies to test paired CREs in alternative orientations, TFBS-perturbed variants of developmental CREs, and literature-selected CRE controls. The table combines the author-provided cluster-level activity summaries into one long-form table.
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
Embryoid body differentiation, day 21 endpoint
A v2 piggyBac scQer library measured native CRE pairs, orientation variants, TFBS perturbation variants and literature controls at single-cell resolution. Activity is the median mBC UMI signal per cell across biological replicates for each cell cluster.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (15 of 15)
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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 · 15 definitions
construct_class
Long-form class indicating paired, orientation, mutated or literature-selected construct.
element_id
Construct or paired-CRE identifier.
left_element_id
Upstream/left CRE component for a paired construct.
right_element_id
Downstream/right CRE component for a paired construct.
original_element_id
Unmutated CRE identifier for a mutated construct.
mutation_class
Author mutation class, such as WT, high-affinity or low-affinity TFBS perturbation.
mutation_list
List of sequence substitutions for the variant.
variant_sequence
Variant CRE sequence with the source cloning handles.
right_orientation
Orientation of the right CRE in paired orientation constructs.
left_orientation
Orientation of the left CRE in paired orientation constructs.
activity_norm_mBC_umi
Median normalized mBC UMI activity across biological replicates.
cell_cluster
Cell cluster in which the activity was summarized.
detected_reporters
Number of detected reporter constructs contributing to the row.
qc_pass
TRUE for rows passing the ingestion QC filters.
source_table
Supplementary source table or tables used to create the row.
Quality control
The author-provided summary tables were retained when activity was finite and at least one reporter was detected. Zero activity values were retained because they represent valid inactive measurements rather than missing data.
Curation notes
Four author sheets are combined: paired orientations, paired CREs, mutated CREs and literature-selected CREs. Mutation annotations and sequences are joined by the source variant identifier; the raw v2 scQer count matrices are preserved in raw_data/geo.