MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues

BMC Systems Biology

Table 1 Summary of miRNA reads and library information.

Library	# of reads analyzed	# of miRNA reads	% miRNA reads	# of detected pre-miRNAs	# of detected miRNAs	# of detected miRNAs at opposite arm	Description
SRX018957	8,057,617	7,025,801	87.19%	381	475	42	Normal
SRX018958	11,234,315	10,241,350	91.16%	439	555	62	Normal
SRX018959	10,035,888	9,229,254	91.96%	424	535	65	Normal
SRX018960	8,493,004	7,424,150	87.41%	400	486	39	HBV(+)
SRX018961	8,214,755	7,290,360	88.75%	507	609	82	Severe HBV(+)
SRX018962	7,413,793	5,767,890	77.80%	417	519	48	HBV(+) distal
SRX018963	8,214,714	6,623,536	80.63%	418	529	51	HBV(+) adjacent
SRX018964	8,042,722	6,668,203	82.91%	426	540	44	HBV(+) side
SRX018965	7,859,049	6,332,172	80.57%	472	598	64	HBV(+) HCC
SRX018966	10,640,841	8,683,683	81.61%	467	596	60	HBV(+) adjacent
SRX018967	10,979,156	9,790,644	89.17%	465	584	64	HBV(+) HCC
SRX018968	5,686,232	3,663,927	64.44%	443	556	58	HCV(+) adjacent
SRX018969	9,224,742	4,754,658	51.54%	430	521	68	HCV(+) HCC
SRX018970	8,967,260	7,618,011	84.95%	407	519	56	HBV(-) HCV(-) adjacent
SRX018971	9,102,563	7,259,865	79.76%	546	682	112	HBV(-) HCV(-) HCC

We mapped the sequence reads back to human pre-miRNAs, quantifying the expression levels of pre-miRNAs, mature miRNAs and isomiRs. According to miRBase 16, 730 out of the 1,048 human pre-miRNAs encode only one mature miRNA at one arm, either 5p or 3p arm. With the improvement on NGS's sequencing depth, we also detected the opposite-arm mature miRNAs at the pre-miRNAs originally annotated to encode only one miRNA. HBV, HCV and HCC are abbreviations of hepatitis B virus, hepatitis C virus and hepatocellular carcinoma, respectively. Distal, adjacent and side mean that the sites at which the tissues were sampled were >10cm, 2-5cm and 0-2cm far from the HCC sites.

ISSN: 1752-0509