Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

BMC Genomics

Table 1 Analysis of performance for multiple RNA-Seq methods

	mRNA-Seq	RiboZero-Seq	DSN-Seq	RiboZero-FFPE	DSN-FFPE
UNC dataset
Sample size	11	11	10	8	4
% rRNA relative to mRNA-seq	1	5.04	116	7.14	585
	(1–1)	(1.42-8.66)	(78.9-154)	(3.48-10.8)	(-347-1,517)
% Aligned bases	94	93.8	85.5	81.5	93.5
	(91.5-96.5)	(92–95.5)	(82.6-88.4)	(71–92)	(92.2-94.8)
Median CV coverage	0.533	0.525	0.56	0.744	0.929
	(0.506-0.56)	(0.505-0.545)	(0.549-0.57)	(0.713-0.775)	(0.814-1.04)
Median 5′ to 3′ bias	0.27	0.64	0.209	0.356	0.242
	(0.189-0.35)	(0.493-0.788)	(0.143-0.275)	(0.285-0.427)	(0.0329-0.451)
Pearson correlation to microarray	0.851	0.832	0.855	0.636	0.7
	(0.825-0.878)	(0.809-0.854)	(0.84-0.871)	(0.601-0.671)	(0.628-0.771)
TCGA dataset
Sample size	10	6	NA	18	10
% rRNA relative to mRNA-seq	1	11.2	NA	0.935	41.7
	(1–1)	(1.51-20.9)		(0.631-1.24)	(22.1-61.3)
% Aligned bases	96.4	95.0	NA	93.4	93.2
	(95.4-97.5)	(93.9-96.2)		(91.6-95.2)	(90.7-95.8)
Median CV coverage	0.534	0.478	NA	0.83	0.953
	(0.517-0.551)	(0.458-0.499)		(0.791-0.869)	(0.896-1.01)
Median 5′ to 3′ bias	0.309	0.46	NA	0.417	0.157
	(0.244-0.374)	(0.37-0.551)		(0.253-0.581)	(0.0856-0.229)

Five different analyses were performed in order to assess the capabilities of the different RNA-seq protocols. These included: 1) % rRNA relative to mRNA-Seq; 2) % Aligned bases; 3) Median CV coverage; 4) Median 5′ to 3′ bias; 5) The Pearson correlation coefficient between the RNA-Seq libraries methods and the same samples assayed by DNA microarray in UNC dataset.

ISSN: 1471-2164