SORT1 enhancer independent-library replicate saturation-mutagenesis MPRA
Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolutionAn independently constructed 600-bp SORT1 enhancer saturation-mutagenesis library was tested in HepG2 human hepatoblastoma cells 24 hours after plasmid transfection.
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; independent library replicate
Episomal enhancer saturation-mutagenesis MPRA using the pGL4.23c reporter configuration and a 600-bp construct. Error-prone PCR introduced sequence variants and a 15- or 20-bp random tag in the reporter 3′ UTR; tag-to-variant associations were learned by sequencing. Matched DNA and reporter-RNA tag counts were UMI-counted and fitted with the authors’ multiple linear regression model. The source table is aggregated across three independent transfection replicates; this condition’s reported mean replicate Pearson r is 0.98.
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 · 15 definitions
- variant_id
- Variant key formatted as chr:position:reference>alternate; alternate - denotes a one-base deletion.
- element
- Regulatory element or gene promoter tested in this experiment.
- chromosome
- Chromosome from the GRCh37/hg19 source table, with chr prefix added.
- position_grch37
- 1-based GRCh37/hg19 genomic position of the reference base.
- reference_allele
- Reference nucleotide in the assayed construct.
- alternate_allele
- Substituted nucleotide or - for a one-base deletion.
- variant_type
- SNV for a single-nucleotide substitution or 1-bp deletion.
- tag_count
- Number of associated random sequence tags supporting the fitted variant effect.
- dna_count
- Aggregate plasmid-DNA tag UMI count reported in the source table.
- rna_count
- Aggregate reporter-RNA tag UMI count reported in the source table.
- log2_effect
- Fitted variant effect coefficient (log2 RNA/DNA activity effect relative to the reference sequence).
- fold_change
- 2 raised to log2_effect, representing the estimated activity fold change relative to the reference sequence.
- p_value
- Source coefficient-fit p-value for the fitted variant effect; not multiple-testing adjusted.
- significant_p_lt_1e-5
- Boolean flag for the paper’s p-value threshold of less than 1e-5.
- source_table
- Original OSF source table filename used to create this row.
Quality control
The authors required tag-to-variant assignment reads to have at least 3-fold coverage across the full construct, counted each tag×UMI pair once, retained tags observed in both DNA and RNA, and required at least 10 associated tags per variant for downstream model fitting. Package QC additionally removed rows with missing/invalid GRCh37 variant fields, non-positive DNA/RNA counts, non-finite effect or p-value fields, and duplicate variant keys. Of 1998 source rows, 1918 passed and 80 were excluded ({'below_minimum_tags': 80, 'invalid_variant_fields': 0, 'invalid_counts': 0, 'invalid_effect_or_p_value': 0, 'duplicate_variant': 0}). Non-significant variants are retained when they pass QC; significant_p_lt_1e-5 records the paper’s p-value threshold.
Curation notes
Source: GRCh37_SORT1.2.tsv from the authors’ OSF project (https://osf.io/download/5bfc220b737718001a084364/). The source table had 1998 rows and the processed table has 1918 rows after QC. The source reports aggregate counts/effects across three transfection replicates rather than replicate-level rows. SORT1.2 is an independently constructed saturation-mutagenesis library assayed on a different culture/day from SORT1.