LTV1 replicate 2 synthetic saturation-mutagenesis enhancer MPRA in mouse liver
Massively parallel functional dissection of mammalian enhancers in vivoA 302-bp candidate mouse LTV1 enhancer (mm9 chr7:29161443-29161744) was synthesized using the second independent overlapping-oligonucleotide design 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 906 possible single-nucleotide substitutions in LTV1 replicate 2.
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. Two independently assembled LTV1 oligonucleotide designs were pooled, aliquoted into independent libraries, and associated with different tag sets; this experiment is the second library (ltv1-2). 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 tag-normalized numbers of RNA pools in which a haplotype was observed, and the 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; LTV1_rep_2 for this experiment.
- position_1based
- 1-based position within the 302-bp enhancer sequence.
- genomic_coordinate
- 1-based mm9 genomic coordinate corresponding to the enhancer position.
- wild_type_base
- Reference nucleotide at the position in the LTV1 construct reference, reconstructed from the article’s PCA oligonucleotides; the construct differs from the UCSC mm9 interval at position 125.
- 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 LTV1 replicate-2 library contained complete representation of the 906 possible substitutions, with each substitution present in at least 42 uniquely tagged haplotypes. For LTV1, pool counts for a haplotype were normalized by the number of tags associated with that haplotype. The two independently constructed LTV1 libraries were highly reproducible (r=0.96), and the published models were fit separately to each library after pooling mouse data. Package QC retained rows with the expected enhancer label, positions 1–302, A/C/G/T mutant bases, finite coefficients, and p values in [0,1]; all 906 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 302 positions and three alternative nucleotides (906 rows) from the publisher’s ltv1-2 records. 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 were reconstructed from the article’s PCA oligonucleotides and genomic coordinates were assigned using the article’s mm9 interval; the construct reference differs from UCSC mm9 at position 125 (A in the construct versus G in UCSC). 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.