Table 2.

Sequencing platforms, chemistries and library preparations.

Illumina Hiseq2000/2500 and MiSeq
Labs	Samples	Libraries per Sample	Preparation	Read Length	Number of Reads per Library	Output (Mb)
1(L)	MAQC A 1	3	Ribo-depleted	100 bp (2 x 50)	386,726,967	38,673
	MAQC B 1	3	Ribo-depleted	100 bp (2 x 50)	251,724,566	25,172
2(R)	MAQC A 1	3	Ribo-depleted	100 bp (2 x 50)	229,131,233	22,913
	MAQC B 1	3	Ribo-depleted	100 bp (2 x 50)	229,591,730	22,959
	MAQC B 1	1	Ribo-depleted	500 bp (2 x 250)	7,848,217	3,924
3(V)	MAQC A 1	3	Ribo-depleted	100 bp (2 x 50)	207,603,620	20,760
	MAQC B 1	3	Ribo-depleted	100 bp (2 x 50)	239,930,780	23,993
4(N)	MAQC A 1,3	2	Ribo-depleted	100 bp (2 x 50)	215,903,801	21,590
	MAQC B 1,3	3	Ribo-depleted	100 bp (2 x 50)	219,257,190	21,926
	MAQC A 1,4	1	Ribo-depleted	100 bp (2 x 50)	183,811,383	18,381
5(M)	MAQC A 1,4	3	Ribo-depleted	100 bp (2 x 50)	386,726,967	38,673
	MAQC A 1,5	3	Ribo-depleted	100 bp (2 x 50)	181,740,643	18,174
6(W)	MAQC A 2	4	Ribo-depleted	100 bp (2 x 50)	128,133,887	12,813
	MAQC B 2	4	Ribo-depleted	100 bp (2 x 50)	137,096,343	13,710
	MAQC C 2	4	Ribo-depleted	100 bp (2 x 50)	142,135,538	14,214
	MAQC D 2	4	Ribo-depleted	100 bp (2 x 50)	128,040,437	12,804
	MAQC A 2	4	polyA-enriched	100 bp (2 x 50)	106,762,840	10,676
	MAQC B 2	4	polyA-enriched	100 bp (2 x 50)	111,430,017	11,143
	MAQC C 2	4	polyA-enriched	100 bp (2 x 50)	108,582,900	10,858
	MAQC D 2	4	polyA-enriched	100 bp (2 x 50)	105,978,082	10,598

Life Technologies Ion Torrent PGM and Proton
Labs	Samples6	Libraries per Sample	Preparation7	Median Read Length	Mean Number of Reads	Output (Mb)
1(P) Ion PGM	MAQC A	2	polyA-enriched	161	5,323,672	857
	MAQC B	2	polyA-enriched	184	5,802,563	107
	ERCC 1	1	polyA-enriched	189	4,188,385	792
	ERCC 2	1	polyA-enriched	158	3,231,475	511
	ERCC 1	1	polyA-enriched	180	4,442,093	800
	ERCC 2	1	polyA-enriched	189	4,310,663	815
2(H) Ion PGM	MAQC A	3	polyA-enriched	128	3,374,068	445
	MAQC B	3	polyA-enriched	129	3,409,662	436
	ERCC 1	2	polyA-enriched	152	2,538,594	810
	ERCC 2	2	polyA-enriched	112	2,119,884	514
	VL A	1	polyA-enriched	187	3,965,022	770
	VL B	1	polyA-enriched	162	4,138,326	687
3(S) Ion PGM	MAQC A	3	polyA-enriched	198	5,049,998	1,000
	MAQC B	3	polyA-enriched	199	5,743,028	1,140
	ERCC 1	1	polyA-enriched	206	6,835,287	1,410
	ERCC 2	2	polyA-enriched	207	7,119,023	1,480
	ERCC 1	1	polyA-enriched	182	6,525,478	1,190
	ERCC 2	1	polyA-enriched	191	5,490,495	1,050
4(S) Proton	MAQC A	3	polyA-enriched	78	50,063,784	3,900
	MAQC B	3	polyA-enriched	85	53,203,028	4,497
5(B) Proton	MAQC A	1	polyA-enriched	95	57,701,947	4,864
	MAQC B	1	polyA-enriched	75	39,099,605	2,946
	MAQC C	1	polyA-enriched	64	41,308,206	6412,641
	MAQC D	1	polyA-enriched	53	46,665,851	3,160
6(L) Proton	MAQC A	1	polyA-enriched	99	60,106,614	5,978
	MAQC B	1	polyA-enriched	100	60,769,231	6,085
	MAQC C	1	polyA-enriched	107	60,353,696	6,454
	MAQC D	1	polyA-enriched	106	69,977,984	7,413

Pacific Biosciences RS
Labs	Samples	Libraries per Sample: Size Fractionation	Preparation8	Avg. Read Length	Reads/Mb	Output (Mb)
1(A)	MAQC A	1: >3 kb	polyA + 5'G cap	3,983	251	663
	MAQC A	1: 2-3 kb	polyA + 5'G cap	3,513	284	520
	MAQC A	1: 1-2 kb	polyA + 5'G cap	2,811	356	780
	MAQC B	1: >3 kb	polyA + 5'G cap	3,467	288	536
	MAQC B	1: 2-3 kb	polyA + 5'G cap	3,223	310	459
	MAQC B	1: 1-2 kb	polyA + 5'G cap	3,112	321	638
2(F)	MAQC A	1: >3 kb	polyA + 5'G cap	3,472	288	634
	MAQC A	1: 2-3 kb	polyA + 5'G cap	3,644	274	555
	MAQC A	1: 1-2 kb	polyA + 5'G cap	2,792	358	927
	MAQC A	1: unfractionated	polyA + 5'G cap	2,832	353	260
	MAQC B	1: >3 kb	polyA + 5'G cap	3,578	280	667
	MAQC B	1: 2-3 kb	polyA + 5'G cap	3,523	284	594
	MAQC B	1: 1-2 kb	polyA + 5'G cap	2,844	351	991
	MAQC B	1: unfractionated	polyA + 5'G cap	2,814	355	251
3(H)	MAQC A	1: >3 kb	polyA + 5'G cap	3,201	312	528
	MAQC A	1: 2-3 kb	polyA + 5'G cap	3,135	319	344
	MAQC A	1: 1-2 kb	polyA + 5'G cap	2,761	362	767
	MAQC A	1: unfractionated	polyA + 5'G cap	2,998	334	477
	MAQC B	1: >3 kb	polyA + 5'G cap	3,189	314	572
	MAQC B	1: 2-3 kb	polyA + 5'G cap	2,952	339	383
	MAQC B	1: 1-2 kb	polyA + 5'G cap	2,779	360	660
	MAQC B	1: unfractionated	polyA + 5'G cap	3,069	326	395

Roche 454 FLX
Labs	Samples	Libraries per Sample	Preparation9	Median Read Length	Total Reads per PicoTiterPlate	Output (Mb)
1(I)	MAQC A	1	polyA-enriched	520	1,061,320	552
	MAQC B	1	polyA-enriched	494	1,001,678	495
	MAQC A	1	polyA-enriched	497	805,399	400
	MAQC B	1	polyA-enriched	496	1,076,634	534
2(P)	MAQC A	1	polyA-enriched	455	832,580	379
	MAQC B	1	polyA-enriched	470	1,181,610	555
3(C)	MAQC A	2	polyA-enriched	505	1,294,497	654
	MAQC B	2	polyA-enriched	358	293,471	105

¹Illumina RNA TruSeq v2 library kit,

²Illumina RNA TruSeq v3 library kit,

³RNaseA degraded,

⁴heat degraded,

⁵sonicated

⁶ERCC: synthetic standards only (External RNA Control Consortium); VL: pilot data for sample A or B;

⁷Ion Total RNA-Seq v2 library kit

⁸PacBio Large Insert Template Prep Kit

⁹Roche cDNA Rapid Library kit