Table 1.

Effect of alignment reference on read quantification.

Alignment reference	Condition	Total aligned reads (x 1000)	Quantified reads (x1000)	# of Unique miRNA quantitated
a. RefSeq quantitation
Whole Genome	NSC	3,482 ± 434	2,735 ± 320	1776
	sip63	2,979 ± 487	2,328 ± 406	1816
RefSeq	NSC	2,681 ± 292	2,681 ± 292	1874
	sip63	2,295 ± 398	2,295 ± 398	1873
miRBase	NSC	676 ± 113	676 ± 116	1802
	sip63	526 ± 138	526 ± 138	1806
b. miRBase quantitation
Whole Genome	NSC	3,482 ± 434	1,039 ± 59	1327
	sip63	2,979 ± 487	661 ± 124	1309
RefSeq	NSC	2,681 ± 292	1,080 ± 59	2241
	sip63	2,295 ± 398	705 ± 130	2276
miRBase	NSC	676 ± 116	676 ± 116	2582
	sip63	526 ± 138	526 ± 138	2586

Raw reads from NSC or sip63 samples trimmed to a fixed length based on quality score were aligned to the whole genome, RefSeq, or miRBase references and quantitated using either (a) RefSeq or (b) miRBase reference. The total number of aligned reads indicate the total number available for quantitation. The number of quantified and unique reads obtained using each of these methods is also indicated.