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Table 1 Datasets

From: Linear models enable powerful differential activity analysis in massively parallel reporter assays

Dataset Description Cell culture Replicates Barcodes
Differential analysis: alleles    
Tewhey Study of 39,479 oligos coming from 29,173 variants NA12878 (LCL) NA12878: 5 79k pool: 73
  to follow up on prior eQTL results. NA19239 (LCL) NA19239: 3 7.5k pool: 350
  Large initial oligo pool: 79k. Second pool: 7.5k. HepG2 HepG2: 5  
Ulirsch Study of 2756 variants in strong LD with 75 main K562, K562 with K562: 6 14
  variants to identify loci that affect RBC traits. GATA1 over-expr. K562+GATA1: 4  
Differential analysis: conditions    
Inoue Comparison of episomal and lentiviral MPRA. HepG2 3 Max: 99
Shen Study of tissue specificity of cis-regulatory Mouse retina and 3 8
  element in-vivo in mouse. cerebral cortex   
Saturation mutagenesis    
Melnikov Two inducible enhancers: HEK293T Single: 2 Single: 13
  (1) a synthetic cAMP-regulated enhancer and   Multi: 2 Multi: 1
  (2) the virus-inducible interferon-beta enhancer.    
  Single-hit scanning alters one base at a time.    
  Multi-hit sampling alters several bases at a time.    
Kheradpour Study of 2104 wild-type sequences and 3314 variant K562 2 10
  sequences containing targeted motif disruptions to HepG2   
  understand base-level effects in motifs.    
  1. All datasets are publicly available, see the relevant publication