ALDOB synthetic saturation-mutagenesis enhancer MPRA in mouse liver
Massively parallel functional dissection of mammalian enhancers in vivoA 259-bp human intronic ALDOB enhancer (hg19 chr9:104195570-104195828) was synthesized as a randomly doped haplotype library and cloned into a tagged luciferase reporter plasmid. The library was delivered to CD1 mouse liver by hydrodynamic tail-vein injection, and the processed table contains the published effect estimates for all 777 possible single-nucleotide substitutions.
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
Hydrodynamic tail-vein delivery; no exogenous biological treatment; 24 h post-injection harvest
In vivo episomal MPFD assay using a randomly doped (~97:1:1:1) synthetic enhancer haplotype library in the pGL4.23 luciferase reporter. A fully degenerate 20-bp tag was placed in the luciferase 3′ UTR; 10 µg library plus 2 µg pGL4.74[hRluc/TK] injection-control plasmid was introduced into CD1 mice by hydrodynamic tail vein injection. After 24 h, tag cDNA was sequenced on Illumina GAIIx. Activity was represented by the number of RNA pools in which a tag-associated haplotype was observed, and the primary allele-level values are the authors’ position-specific trivariate linear-regression coefficients expressed as log2 fold change relative to wild type.
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 · 10 definitions
- element_id
- Enhancer library identifier; ALDOB for this experiment.
- position_1based
- 1-based position within the 259-bp enhancer sequence.
- genomic_coordinate
- 1-based hg19 genomic coordinate corresponding to the enhancer position.
- wild_type_base
- Reference nucleotide at the position, added from the UCSC hg19 sequence for the article’s coordinate interval.
- mutant_base
- Specific alternative nucleotide tested by the trivariate model; supplied by the publisher’s Supplementary Data.
- mutation_id
- Stable human-readable identifier combining enhancer, relative position, reference base, and mutant base.
- effect_size_log2_fc
- Published trivariate-model effect size for the specific substitution, expressed as log2 predicted activity fold change relative to wild type.
- p_value
- Published p value for the specific mutant-base coefficient in the trivariate model; not multiple-testing adjusted in the source table.
- position_effect_size_log2_fc
- Published univariate-model effect size for any mutation at the position, expressed as log2 predicted activity fold change relative to wild type.
- position_p_value
- Published p value for the position-level mutation coefficient in the univariate model; not multiple-testing adjusted in the source table.
Quality control
The authors filtered tag reads by quality across the first 20 tag bases and required at least 10 reads to classify a tag as present in an RNA pool. Tag-guided subassembly was used to establish tag–haplotype associations; the resulting library contained complete representation of the 777 possible substitutions, with each substitution present in at least 42 uniquely tagged haplotypes. Biological replicates were highly reproducible (ALDOB r=0.93), so the published positionwise models used data combined across mice. Package QC retained rows with the expected enhancer label, positions 1–259, A/C/G/T mutant bases, finite coefficients, and p values in [0,1]; all 777 source rows passed. Non-significant substitutions were retained because this is a complete saturation map.
Curation notes
The table contains one row for each of 259 positions and three alternative nucleotides (777 rows). The article’s Results says the library was introduced into two mice and the final models combined mouse data; the Online Methods states that each library was injected into at least three mice, which is a source-text inconsistency. Reference bases and genomic coordinates were added from the UCSC hg19 sequence using the article’s interval; mutant bases, effect sizes, and p values come directly from the publisher-supplied full-precision tables. The supplementary data do not provide barcode-level counts or mouse-level output, so the table is coefficient-level rather than count-level. No source rows failed package QC.