Biallelic HAR mutation activity MPRA in primary mouse neurospheres
Mutations in Human Accelerated Regions Disrupt Cognition and Social BehaviorA custom episomal plasmid MPRA tested wild-type and mutant versions of 343 biallelic human accelerated region (HAR) mutations in primary neurospheres derived from E14.5 mouse cortex. The packaged table reports the published normalized WT/MT activity ratio and log2 WT/MT effect for each assayed mutation, alongside genomic, population, and regulatory annotations.
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
Rare biallelic HAR mutations from affected and unaffected individuals were represented by wild-type and mutant probes. Each mutation was tiled with three unique 115-bp ssDNA oligonucleotides overlapping by 90 bp; the pool was cloned into pMPRA1 with a luciferase/minimal-promoter reporter, electroporated into batches of 5 million primary mouse neurosphere cells (2 µg construct; Neon, 1,400 V, 40 ms, 1 pulse), and harvested after 48 h. Tag-seq cDNA was sequenced at 75 bp on Illumina MiSeq; reads were retained only when they passed quality filters and perfectly matched oligo barcodes.
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 · 19 definitions
- variant_id
- Stable variant identifier constructed as chromosome:start:reference>alternate using the hg19 coordinates and alleles reported in Table S7.
- chromosome
- Chromosome with a chr prefix from the Table S7 coordinate.
- start_hg19
- 1-based variant start coordinate on hg19.
- end_hg19
- 1-based variant end coordinate on hg19.
- ref_allele
- Reference allele used to define the reported biallelic mutation; '-' denotes an insertion/deletion anchor as reported.
- alt_allele
- Alternate allele of the reported biallelic mutation; '-' denotes a deletion as reported.
- variant_type
- SNV or INDEL as reported by Table S7.
- functional_annotation
- ANNOVAR Func.refGene functional category for the variant.
- gene_annotation
- ANNOVAR Gene.refGene gene or locus annotation; comma-separated values retain the source annotation.
- max_cadd_or_gerp
- Maximum of the CADD and GERP scores reported in Table S7.
- har_id
- Merged human accelerated region identifier from Table S7.
- homozygous_count
- Number of homozygous individuals reported for the variant.
- homozygous_affected_count
- Number of homozygous affected individuals reported for the variant.
- homozygous_unaffected_count
- Number of homozygous unaffected individuals reported for the variant.
- max_allele_frequency
- Maximum allele frequency reported for the variant.
- brain_neuronal_regulatory_annotation
- Whether the variant overlaps a brain/neuronal enhancer, transcription, or transcription-start-site annotation.
- chromhmm_activity
- Whether the variant overlaps an active ChromHMM regulatory state.
- wt_mt_neurosphere_normalized_ratio
- Published normalized average activity ratio of the wild-type reporter to the mutant reporter in mouse neurospheres; values above 1 indicate lower mutant activity.
- log2_wt_mt_neurosphere_ratio
- Base-2 logarithm of the published WT/MT normalized activity ratio; positive values indicate lower mutant activity and negative values indicate higher mutant activity.
Quality control
The study filtered MPRA reads for quality and perfect matches to oligo barcodes. Package-level QC retained rows only when all required variant, annotation, and activity fields were present, the WT/MT normalized average was positive and finite, and the reported log2 WT/MT value matched log2(WT/MT) within 1e-8; all 343 published Table S7 rows passed these checks. No read counts, replicate-level counts, or statistical significance columns were available in the supplemental workbook, so no additional count-based filter was applied.
Curation notes
This is the study's only MPRA experiment. Table S7 is a published results table rather than a raw barcode-count matrix and contains 343 mutations (242 SNVs and 101 INDELs). The biosample is mapped to CL:0000047 (neural stem cell) because the paper describes primary mouse neurospheres derived from embryonic cortex rather than a purified differentiated neuronal subtype. Coordinates and annotations are carried over from the paper's hg19-based HAR analysis. The paper's N2A/SH-SY5Y luciferase validations and transgenic-mouse assays were not packaged as separate MPRA experiments.