A shared 266-bp episomal MPRA library containing putative cortical cis-regulatory elements and GC-matched scrambled controls was electroporated in utero into mouse somatosensory cortex at E12-E16. Tbr2+ intermediate progenitors were FACS-isolated 24 hours later and profiled as DNA input and RNA output across collection days E13-E17.
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:intermediate_progenitor_cell
Reference genome
mm10
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
In utero electroporation of the MPRA plasmid library; no exogenous treatment
The library design comprised 11,905 putative eCREs and 997 GC-matched scrambled controls; inserts were centered on accessibility peaks and resized to 266 bp. The plasmid pool was electroporated into embryonic somatosensory cortex, followed by Pax6/Tbr2/Tubb3 staining and FACS 24 hours later. DNA and reverse-transcribed RNA barcode libraries were processed with cutadapt/MPRAflow and activity was scored with MPRAnalyze. This child experiment contains the five IPC collection-day columns; the sibling child contains the matched NSC measurements.
Processed data
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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 · 25 definitions
element_id
Source element name from the GEO MPRA table; coordinate-bearing names encode the tested mm10 interval.
library_class
Source enh_type class for the sequence (E14, IPC, Mature, NSC, Scrambled, or Shadow).
chromosome
Chromosome parsed from coordinate-bearing element_id names; blank for index-only library names.
start_mm10
Start coordinate on mm10 parsed from coordinate-bearing element_id names; blank when unavailable.
end_mm10
End coordinate on mm10 parsed from coordinate-bearing element_id names; blank when unavailable.
sequence_length_bp
Tested insert length in base pairs; set to 266 from the paper's MPRA design.
IPC_E13_statistic
Published MPRA statistic for Tbr2+ IPCs collected at E13.
IPC_E14_statistic
Published MPRA statistic for Tbr2+ IPCs collected at E14.
IPC_E15_statistic
Published MPRA statistic for Tbr2+ IPCs collected at E15.
IPC_E16_statistic
Published MPRA statistic for Tbr2+ IPCs collected at E16.
IPC_E17_statistic
Published MPRA statistic for Tbr2+ IPCs collected at E17.
IPC_E13_mad_score
Published MPRAnalyze MAD score for Tbr2+ IPCs collected at E13.
IPC_E14_mad_score
Published MPRAnalyze MAD score for Tbr2+ IPCs collected at E14.
IPC_E15_mad_score
Published MPRAnalyze MAD score for Tbr2+ IPCs collected at E15.
IPC_E16_mad_score
Published MPRAnalyze MAD score for Tbr2+ IPCs collected at E16.
IPC_E17_mad_score
Published MPRAnalyze MAD score for Tbr2+ IPCs collected at E17.
IPC_E13_p_value
Published MPRAnalyze MAD-based p-value for Tbr2+ IPCs collected at E13.
IPC_E14_p_value
Published MPRAnalyze MAD-based p-value for Tbr2+ IPCs collected at E14.
IPC_E15_p_value
Published MPRAnalyze MAD-based p-value for Tbr2+ IPCs collected at E15.
IPC_E16_p_value
Published MPRAnalyze MAD-based p-value for Tbr2+ IPCs collected at E16.
IPC_E17_p_value
Published MPRAnalyze MAD-based p-value for Tbr2+ IPCs collected at E17.
n_valid_timepoints
Number of E13-E17 IPC collection days with numeric statistic, MAD score, and p-value.
n_timepoints_p_lt_0_1
Number of IPC collection days with published MAD-based p-value <0.1; this is a result summary, not the package QC criterion.
min_p_value
Minimum numeric IPC MAD-based p-value across E13-E17.
qc_pass
TRUE for rows retained after package QC requiring at least one complete IPC time-point metric triplet.
Quality control
The authors used MPRAflow/MPRAnalyze, retained elements with an MPRAnalyze P-value <0.1 in at least one time point for downstream analysis, centered MAD scores, and removed two libraries with low correspondence between MPRA and ATAC signal. The GEO TSV is the authors' processed MPRAflow/MPRAnalyze output and preserves non-significant elements for reference. Package QC treated literal NA as missing and retained rows with at least one complete numeric IPC statistic, MAD score, and p-value across E13-E17; 11,670 rows passed and 39 rows with no complete IPC time point were excluded.
Curation notes
The GEO sample titles denote collection ages E13-E17, while library names encode electroporation ages E12-E16. The source table includes six library classes (E14, IPC, Mature, NSC, Scrambled, Shadow); coordinate fields are parsed only when encoded in the source element name, and index-only element names retain blank coordinates. Literal NA values were converted to blank CSV fields. The exact intermediate progenitor cell term was not resolved to a Cell Ontology CURIE, so the biosample uses the required UNMAPPED form. The table includes all valid elements, not only p<0.1 hits, so negative and non-active controls remain available.