SORL1 exon 17 saturation-mutagenesis MPRA in HeLa cells
Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional RegulationThe SORL1 exon 17 eExon library contained 16,483 distinct mutant haplotypes and 16,582 tagged constructs and covered all 1,665 possible single-nucleotide substitutions. The tagged pGL4.23 library was transiently transfected into HeLa cells and RNA-derived tags were sequenced 24 hours later.
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
Transient transfection of 10 µg MPRA library into HeLa cells; 24 h post-transfection harvest
Episomal MPRA using pGL4.23 luciferase reporter plasmids carrying approximately 97:1:1:1 doped eExon haplotypes and a 20-bp degenerate tag in the reporter 3′ UTR. Ten micrograms of library was transfected into 1–2×10^6 HeLa cells; after 24 h, total RNA was purified, mRNA selected, and 16 RT-PCR aliquots per biological duplicate were indexed and sequenced on Illumina GAIIx. Tag–haplotype associations were established by tag-directed subassembly, and substitution effects were estimated by linear regression on the number of RNA aliquots in which each haplotype was observed.
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 · 33 definitions
- variant_id
- Stable identifier combining the eExon, one-based position, reference allele, and alternate allele.
- element_id
- Identifier for the tested eExon library.
- gene
- Gene containing the tested eExon.
- position_in_element
- One-based position within the 555-bp SORL1 eExon test sequence.
- chromosome_hg19
- Chromosome reported for the tested sequence in hg19.
- coordinate_hg19
- One-based hg19 genomic coordinate of the tested position.
- reference_allele
- Wild-type nucleotide at the position.
- alternate_allele
- Specific alternate nucleotide substitution tested by the MPRA model.
- nucleotide_change
- RefSeq-style nucleotide change annotation when provided by the source; NA when unavailable.
- context
- Source sequence context annotation, such as exonic or intronic.
- effect_size_log2fc
- Published HeLa trivariate-model effect size, expressed as log2 predicted activity fold change relative to wild type.
- fold_change
- Linear predicted activity fold change calculated as 2 raised to effect_size_log2fc.
- p_value
- Published unadjusted p-value for the specific substitution effect.
- significant_p_0_05
- Boolean indicating whether the published p-value is at most 0.05; this flag was not used as a row filter.
- effect_direction
- Direction derived from the effect size: increased, decreased, or no_change.
- GERP
- GERP conservation score reported by the source.
- RefSeq
- RefSeq transcript identifier reported by the source.
- exon
- Exon annotation reported by the source.
- amino_acid_change
- Amino-acid consequence annotation reported by the source.
- amino_acid_context
- Synonymous, non-synonymous, stop-codon, or other coding context reported by the source.
- ENCODE_TF_ChIP_seq_peaks
- ENCODE transcription-factor ChIP-seq peak annotation at the position.
- TF_ChIP_seq_in_HEPG2
- HepG2 TF ChIP-seq annotation at the position.
- DNase_I_cluster
- DNase I hypersensitivity cluster indicator from the source.
- SNP135_database
- SNP135 database indicator from the source.
- SIFT_score
- SIFT score reported by the source.
- PolyPhen2_score
- PolyPhen-2 score reported by the source.
- TF_mark
- Transcription-factor motif whose reference-to-mutant mark score change was reported.
- WT_mark_score
- Reference-sequence motif mark score.
- mut_mark_score
- Mutant-sequence motif mark score.
- absolute_score_change
- Absolute difference between mutant and reference motif mark scores.
- relative_entropy
- Relative entropy threshold/score reported for the motif model.
- source_sheet
- Worksheet name in the publisher-supplied Table S5 workbook.
- source_table
- Publisher source table identifier.
Quality control
The authors quality-filtered the first 20 tag bases, counted tag observations, retained tags supported by at least 10 reads, established tag–haplotype links by subassembly, and assessed replicate reproducibility before combining biological duplicates (SORL1 HeLa r=0.85). Package QC retained all 1,665 source rows because each had a valid integer hg19 coordinate, distinct A/C/G/T reference and alternate alleles, finite effect size, and p-value in [0,1]. The paper's p≤0.05 criterion is represented by a boolean column and was not used to remove non-significant substitutions.
Curation notes
HeLa is the human cervical cancer cell line resolved to Cellosaurus CVCL:0030. Table S5 provides mutation-level coefficients and p-values rather than barcode-level DNA/RNA counts; non-significant substitutions are retained so the table remains a complete saturation map. Several annotations are NA for intronic positions because they were not reported by the source.