Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control

Table 1 Genomic categories that are mapped by sRNA reads by size-fractionated total RNA libraries (TAP cloning method)

	Size-fractionated total RNA libraries, 5′ P-independent cloning, WT
Categories	15-30nt (27nt sRNAs)	30-45nt ^# (27nt and 31nt sRNAs)	3'-end trimmed ^* (31nt sRNAs trimmed off oligo-As)
Total reads	624,954	411,419
Unique (unique/total reads)	242,277 (38.8%)	171,309 (41.6%)	86,031
tRNA^a,S	2,343 (1.0%)	2,848 (1.7%)	1,035 (1.2%)
rRNA^a,S	12,957 (5.3%)	18,235 (10.6%)	450 (0.5%)
LINEs^a,AS	16,424 (6.8%)	8,492 (5.0%)	23,999 (27.9%)
Map to rest of genome^a	172,261 (71.1%)	55,703 (32.5%)	36,651 (42.6%)
Map to predicted ORFs^a,AS	124,770 (51.5%)	37,145 (21.7%)	27,508 (32%)
Not mapped to genome (%)	38,292 (15.8%)	86,031 (50.2%)	23,896 (27.8%)

^a Number of unique reads divided by total unique reads
^S Most reads are in sense orientation
^AS Most reads are in antisense orientation
^# Only 27nt sRNAs can be mapped to the genome, not 31nt sRNAs
^* The 31nt sRNAs (non-mapped reads in 30-45nt library) were trimmed from 3' end into 27nt size, then they can be mapped to the genome.

ISSN: 1471-2164