MPRAnalyze: statistical framework for massively parallel reporter assays

Table 1 MPRA datasets used for evaluation of MPRAnalyze throughout the paper

Dataset	Type of analysis	Integration	DNA sequencing	#Sequences	#Negative controls	#Barcodes	#Replicates (DNA,RNA)
Kwasnieski [10]	Quantification	Episomal	Pre-transduction	1200	568	4	1,4
Inoue-Kircher (epi) [9]	Quantification	Episomal	Post-transduction	2338	102	100	3,3
Inoue-Kircher (chr) [9]	Quantification	Lentiviral	Post-transduction	2338	102	100	3,3
Inoue-Kreimer [17]	Comparative	Lentiviral	Post-transduction	2464	200	90	3,3
Mattioli [13]	Allelic Comparison	Episomal	Pre-transduction	3960	0	26/80	1, 4/8

In the Mattioli data, multiple values indicate an asymmetric design: reference alleles were associated with 80 barcodes compared with 26 barcodes for alternative alleles, and 4 replicates were available for K562 cells compared with 8 in HepG2. For further details on each datasets, see “Methods”

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