Experiment / E9GC2XDAWEpisomal Plasmid MPRA

Genomic wild-type/motif-mutant library (gWT/gMUT) in RW4 mouse embryonic stem cells

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells

A plasmid MPRA tested mouse genomic 81–82 bp elements selected for comparable pluripotency-factor binding-site configurations alongside matched sequences in which the primary sites were disrupted. The processed table contains one row per recovered gWT/gMUT coordinate pair.

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: CVCL:6442
Reference genome: mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

pCF10 plasmid libraries carried 81–82 bp mm10-derived genomic sequences or matched gMUT sequences upstream of a minimal Pou5f1 promoter and dsRed/SV40 UTR reporter. Three biological RNA replicates and one shared plasmid-DNA pool were sequenced on Illumina NextSeq; gWT and gMUT activities are normalized RNA-RPM/DNA-RPM ratios relative to basal-promoter controls.

Processed data

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Visible columns (39 of 39)

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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 · 39 definitions

element_id: mm10 coordinate shared by the matched wild-type and motif-mutant constructs.
reference_genome: Mouse reference assembly used for the genomic sequence coordinates.
chromosome: Chromosome parsed from element_id.
start_mm10: 1-based start coordinate parsed from the paper element identifier.
end_mm10: End coordinate parsed from the paper element identifier.
wild_type_element_id: Supplementary design identifier for the genomic wild-type (gWT) construct.
mutant_element_id: Supplementary design identifier for the pluripotency-site-mutated (gMUT) construct.
wild_type_sequence: 81–82 bp mm10-derived genomic sequence in the gWT construct.
mutant_sequence: Matched 81–82 bp sequence with the primary pluripotency TF-binding sites disrupted.
barcode_count_design_wt: Number of designed barcodes for the gWT construct.
barcode_count_design_mut: Number of designed barcodes for the gMUT construct.
barcode_count_qc_wt: gWT barcodes retained after DNA >=10 and all three RNA replicates >=3 raw-read thresholds.
barcode_count_qc_mut: gMUT barcodes retained after DNA >=10 and all three RNA replicates >=3 raw-read thresholds.
dna_count_qc_wt: Sum of raw gWT plasmid-DNA counts over retained barcodes.
dna_count_qc_mut: Sum of raw gMUT plasmid-DNA counts over retained barcodes.
rna_count_qc_wt_rep1: Sum of raw gWT RNA counts over retained barcodes in RNA replicate 1.
rna_count_qc_wt_rep2: Sum of raw gWT RNA counts over retained barcodes in RNA replicate 2.
rna_count_qc_wt_rep3: Sum of raw gWT RNA counts over retained barcodes in RNA replicate 3.
rna_count_qc_mut_rep1: Sum of raw gMUT RNA counts over retained barcodes in RNA replicate 1.
rna_count_qc_mut_rep2: Sum of raw gMUT RNA counts over retained barcodes in RNA replicate 2.
rna_count_qc_mut_rep3: Sum of raw gMUT RNA counts over retained barcodes in RNA replicate 3.
wt_activity_rep1: gWT element activity as mean retained-barcode RNA-RPM/DNA-RPM ratio normalized to basal controls in RNA replicate 1.
wt_activity_rep2: gWT element activity as mean retained-barcode RNA-RPM/DNA-RPM ratio normalized to basal controls in RNA replicate 2.
wt_activity_rep3: gWT element activity as mean retained-barcode RNA-RPM/DNA-RPM ratio normalized to basal controls in RNA replicate 3.
wt_activity_mean: Mean gWT activity across the three RNA biological replicates.
wt_activity_sem_replicates: Standard error of the three gWT replicate activities.
mut_activity_rep1: gMUT element activity as mean retained-barcode RNA-RPM/DNA-RPM ratio normalized to basal controls in RNA replicate 1.
mut_activity_rep2: gMUT element activity as mean retained-barcode RNA-RPM/DNA-RPM ratio normalized to basal controls in RNA replicate 2.
mut_activity_rep3: gMUT element activity as mean retained-barcode RNA-RPM/DNA-RPM ratio normalized to basal controls in RNA replicate 3.
mut_activity_mean: Mean gMUT activity across the three RNA biological replicates.
mut_activity_sem_replicates: Standard error of the three gMUT replicate activities.
wt_minus_mut_activity_mean: Mean gWT activity minus mean gMUT activity; positive values indicate activity dependent on the intact genomic sites.
log2_wt_over_mut_activity_mean: Base-2 logarithm of mean gWT activity divided by mean gMUT activity.
wt_vs_basal_p_rep1: Paper Wilcoxon p-value for gWT versus basal expression in RNA replicate 1.
wt_vs_basal_p_rep2: Paper Wilcoxon p-value for gWT versus basal expression in RNA replicate 2.
wt_vs_basal_p_rep3: Paper Wilcoxon p-value for gWT versus basal expression in RNA replicate 3.
wt_mut_p_value: Paper Wilcoxon p-value for the paired gWT versus gMUT comparison.
wt_mut_significant_0_05: Paper flag for unadjusted gWT/gMUT p < 0.05.
wt_mut_bonferroni_0_05: Paper flag for Bonferroni-adjusted gWT/gMUT p < 0.05.

Quality control

Authors removed barcodes with fewer than 3 raw reads in any RNA replicate or fewer than 10 raw reads in DNA, reporting R² = 0.96–0.98 between gWT/gMUT-library RNA replicates. Package QC retained all 403 recovered gWT elements and 403 fully matched gWT/gMUT pairs with at least one passing barcode on each side; the four gMUT-only design records without a recovered gWT counterpart are excluded from this paired table.

Curation notes

The paper describes 407 genomic wild-type and 407 matched mutant designs, but the public design/count release contains 403 gWT coordinates and 407 gMUT records. The table is intentionally pair-level and includes the 403 complete coordinate pairs used for matched activity comparisons; it does not mix in basal or CMF-Scalar controls. Supplementary file 1H contains repeated trailing summary records for some gWT/gMUT identifiers; the packaged paper p-values use the first record for each unique identifier, while activities are recomputed from the GEO barcode counts.

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