Influence of RNA extraction methods and library selection schemes on RNA-seq data

BMC Genomics

Table 2 Transcript coverage

	Categories	PolyA Tot RNA Trizol	PolyA Tot RNA Qiagen	RiboZeroTot RNA Trizol	RiboZeroTot RNA Qiagen	RiboZero Cytopl. RNA	RiboZero Nuclear RNA
Protein coding genes	Genes with rpkm ≥ 0.5	12469	12381	12164	12164	12119	12498
	Average genes coverage	67%	65%	69%	68%	65%	71%
	Genes not covered	2259	2447	2016	2085	2316	1778
	Genes ≥50% covered	14345	14144	14540	14540	14038	14978
	Genes 100% covered	1677	1468	2287	2072	1370	2892
	Genes with only 1 read	263	1468	278	292	287	261
	Genes with ≥5 reads	16926	1468	17164	17067	16844	17464
	Genes with ≥50 reads	14768	14667	14812	14836	14597	15190
	Genes with ≥100 reads	14111	14049	13997	14071	13888	14309
Long non-coding RNAs	processed transcript	423	418	452	417	404	532
	lincRNA	596	543	625	546	521	927
	antisense	914	850	748	748	722	911
	sense intronic	97	68	269	269115	87	499
	sense overlapping	58	44	57	42	44	87
	3 prime overlapping ncrna	20	20	19	19	20	22
	non coding	4	3	4	4	4	5

The upper panel lists the number of detected and covered protein coding genes in each category and experimental condition. The panel below lists for each experimental condition the number of detected long non-coding RNA subtypes (rpkm > =0.5).

ISSN: 1471-2164