Human mammary epithelial cell lentiMPRA
Functional analysis of cancer-associated germline risk variantsIntegrated lentiMPRA of 140-bp hg19 SNV-centered genomic fragments with matched reference and alternate alleles, ten 20-bp barcodes per allele, and a minimal-promoter luciferase reporter in Human mammary epithelial cells (Lonza). Three biological replicates were sequenced as RNA barcode counts and normalized to two plasmid DNA library replicates.
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
A single Agilent oligo library was cloned into the pGreenFire-mCMV lentiviral reporter backbone. Each reference/alternate 140-bp genomic fragment carried ten randomly generated 20-bp barcodes; cells were puromycin-selected after transduction, poly(A) RNA barcode counts were measured, and the authors used MPRAnalyze quantitative and comparative models.
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 · 42 definitions
- alt_activity_mean
- Mean of the three alternate RNA/DNA activity estimates
- alt_activity_rep1
- Library-size-normalized alternate RNA/DNA activity estimate in replicate 1 with a 0.5-count pseudocount
- alt_activity_rep2
- Library-size-normalized alternate RNA/DNA activity estimate in replicate 2 with a 0.5-count pseudocount
- alt_activity_rep3
- Library-size-normalized alternate RNA/DNA activity estimate in replicate 3 with a 0.5-count pseudocount
- alt_allele
- Alternate allele used in the MPRA construct
- cancer_type
- Cancer type(s) associated with the tested SNV in the authors' source table
- cell_types_with_differential_activity
- Cell types with significant differential allelic activity
- chr_hg19
- Chromosome in hg19
- da_snv_cancer_type
- Cancer type annotation for a differentially active SNV (daSNV)
- dna_barcode_n_alt
- Alternate-allele barcodes with nonzero count in either plasmid DNA replicate
- dna_barcode_n_ref
- Reference-allele barcodes with nonzero count in either plasmid DNA replicate
- dna_umi_count_alt
- Total alternate-allele plasmid DNA counts across both plasmid replicates
- dna_umi_count_ref
- Total reference-allele plasmid DNA counts across both plasmid replicates
- eqtlgen_egenes
- eQTLGen eGenes associated with the SNV
- gtex_tissue_specific_egenes
- GTEx tissue-specific eGenes associated with the SNV
- gwas_pubmed_id
- PubMed identifier for the associated GWAS study
- gwas_risk_allele
- Risk allele annotation for the GWAS lead SNP
- h3k27ac_hichip_cell_type
- Cell type for the H3K27ac HiChIP contact annotation
- h3k27ac_hichip_ptgenes
- Putative target genes whose promoters contact the SNV in H3K27ac HiChIP
- lead_snp
- Associated GWAS lead SNP
- lead_snp_or_beta
- GWAS lead-SNP odds ratio or beta
- locus_ids
- Raw GEO locus name(s) joined to this variant allele pair
- maf_eur
- European-ancestry minor allele frequency from HaploReg
- mpra_fdr
- Authors' MPRAnalyze FDR for differential allelic activity
- mpra_hit
- 1 when authors' MPRA FDR is <0.05, otherwise 0
- mpra_log2_ref_over_alt
- Authors' MPRAnalyze comparative log2(reference activity/alternate activity)
- nearby_genes
- Genes within 5 kb of the SNV
- position_hg19
- SNV position in hg19
- raw_log2_ref_over_alt
- Descriptive log2(reference activity/alternate activity) from GEO counts
- ref_activity_mean
- Mean of the three reference RNA/DNA activity estimates
- ref_activity_rep1
- Library-size-normalized reference RNA/DNA activity estimate in replicate 1 with a 0.5-count pseudocount
- ref_activity_rep2
- Library-size-normalized reference RNA/DNA activity estimate in replicate 2 with a 0.5-count pseudocount
- ref_activity_rep3
- Library-size-normalized reference RNA/DNA activity estimate in replicate 3 with a 0.5-count pseudocount
- ref_allele
- Reference allele used in the MPRA construct
- rna_umi_count_alt_rep1
- Alternate RNA barcode count in biological replicate 1
- rna_umi_count_alt_rep2
- Alternate RNA barcode count in biological replicate 2
- rna_umi_count_alt_rep3
- Alternate RNA barcode count in biological replicate 3
- rna_umi_count_ref_rep1
- Reference RNA barcode count in biological replicate 1
- rna_umi_count_ref_rep2
- Reference RNA barcode count in biological replicate 2
- rna_umi_count_ref_rep3
- Reference RNA barcode count in biological replicate 3
- rs_id
- dbSNP identifier of the tested variant
- variant_id
- Unique tested allele pair identifier in the form rsID:reference>alternate
Quality control
The authors removed GM12878 and H9 from downstream analysis because more than 35% of barcodes were missing in all replicates (mean 44% and 46%, respectively) and more than 20% of sequences had 5 or fewer represented barcodes. The processed table further retains only unique allele pairs from Supplementary Table 5 that match the GEO raw-count locus key and have at least 5 nonzero plasmid-DNA barcodes for each allele; exact duplicate source rows were collapsed. Authors' comparative MPRA hits are defined as MPRAnalyze FDR <0.05. Count-derived activities use library-size normalization and a 0.5-count pseudocount.
Curation notes
Human mammary epithelial cells; GEO samples GSM5555257, GSM5555258, and GSM5555259. Raw count columns are hmec_1, hmec_2, and hmec_3; the GEO matrix labels its two plasmid DNA columns plasmid_1 and plasmid_2. The source workbook reports the official MPRAnalyze effect/FDR, while raw_* columns are independently summarized from GEO barcode counts. QC summary: 4385 source rows, 4383 unique ref/alt pairs, 46 without a matching raw locus, 62 failed the plasmid-DNA/barcode filter, and 4275 retained in this table.