CRE-seq saturation mutagenesis of mouse RhoCRE3 in newborn retinal explants
Complex effects of nucleotide variants in a mammalian cis-regulatory elementA barcoded plasmid library tested the wild-type mouse RhoCRE3 cis-regulatory element, all 156 single-nucleotide substitutions, and 819 selected double substitutions in explanted newborn mouse retinas. Reporter activity was measured from barcode RNA/DNA ratios after eight days in culture; the processed table contains the published variant-level summary after removing rows with missing activity statistics.
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.
Perturbation & assay details
Basal / Untreated
CRE-seq used transient plasmid electroporation of newborn mouse retinal explants. Each RhoCRE3 variant was placed upstream of a native Rho minimal promoter driving DsRed, with a unique 9-bp barcode in the DsRed 3′ UTR; cDNA and plasmid-DNA barcode sequencing produced copy-number-adjusted RNA/DNA expression values. The paper also reports a separate 120-construct fluorescence comparison, which is not represented as a second experiment because the packaged table is the primary MPRA library.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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
- variant_id
- Published RhoCRE3 variant identifier; wt is the wild-type control and identifiers such as 01A or 40A_49C encode one-based position(s) and alternate base(s).
- variant_class
- Variant category inferred from the identifier: wild_type, single_substitution, or double_substitution.
- mutation_count
- Number of substitutions encoded by the variant identifier.
- wild_type_sequence
- 52-bp wild-type RhoCRE3 sequence at mm9 chr6:115881830-115881881, 5′ to 3′.
- mutant_sequence
- Variant sequence generated by applying the encoded alternate base(s) to wild_type_sequence; identical to wild type for the wt row.
- mutation_1_position
- One-based RhoCRE3 position of the first substitution; blank for wt.
- mutation_1_reference
- Wild-type base at mutation_1_position from the mm9 reference sequence; blank when not applicable.
- mutation_1_alternate
- Alternate base for the first substitution as encoded by the published variant identifier; blank when not applicable.
- mutation_2_position
- One-based RhoCRE3 position of the second substitution; blank for wt and single substitutions.
- mutation_2_reference
- Wild-type base at mutation_2_position from the mm9 reference sequence; blank when not applicable.
- mutation_2_alternate
- Alternate base for the second substitution as encoded by the published variant identifier; blank when not applicable.
- mean_expression
- Published mean cDNA/DNA expression ratio for the variant, aggregated across its barcodes and three biological replicates.
- mean_expression_sem
- Published propagated standard error of the mean expression ratio.
- relative_wt_expression
- Published mean expression normalized to the wild-type RhoCRE3 control.
- relative_wt_expression_sem
- Published standard error for the expression value relative to wild type.
- log2_relative_wt_expression
- Derived log2(relative_wt_expression) activity effect; this transformation is not an additional published statistic.
Quality control
The authors counted reads matching the first 20 nucleotides of designed sequences regardless of quality score and retained only barcodes with >10 reads in either the cDNA or DNA pool. Variant activity was summarized across all barcodes assigned to each variant and three biological replicates; the paper reports high replicate reproducibility (R² = 0.95). Package-level QC retained rows with finite, positive expression and complete published SEM fields. Four source rows with NA activity/SEM values were excluded: 30G_51G, 32G_50C, 40A_48G, and 40A_49C. Thus 972 of 976 variant-summary rows passed the documented QC filter.
Curation notes
The source supplement sd01.txt is a directly usable variant-level summary with one wt, 156 single-mutant, and 819 double-mutant records. The paper states that the library contained 5,720 distinct reporter genes, with ten barcodes per single mutant and five per double mutant. Reference and mutant sequences in table.csv were expanded from the paper's position-plus-alternate-base identifiers using the stated mm9 interval; no rs identifiers apply because these are designed substitutions rather than naturally occurring variants. The publisher also lists sd02.txt as a barcode-level companion dataset, but the packaged table intentionally uses the variant-level summary and does not represent raw sequencing reads.