New methods for next generation sequencing based microRNA expression profiling

BMC Genomics

Table 1 EmiR data processing table

	EMtot-single	EMs-single	EMs-multi	HTs-single	HTs-multi
Input	5,794,222	5,294,849	4,042,101	6,517,852	3,292,684
< 15 nt	2,979,930	2,368,163	2,011,435	3,027,338	1,596,093
≥15 nt	2,814,292	2,926,686	2,030,666	3,490,514	1,696,591
NM	577,710	569,163	294,637	921,828	467,263
R*	967,090	1,138,353	814,299	1,383,114	653,343
U0	684,178	571,752	477,298	578,162	295,420
U1	439,677	472,181	333,808	428,136	201,149
U2	145,637	175,237	110,624	179,274	79,416
U0&U1	1,123,855	1,043,933	811,106	1,006,298	496,569
miRNA	557,167 [49.58%]	765,899 [73.37%]	586,779 [72.34%]	442,242 [43.95%]	215,293 [43.36%]
miscRNA	2,934 [0.26%]	1,341 [0.13%]	981 [0.12%]	3,590 [0.36%]	1,849 [0.37%]
pseudogene	10 [0%]	14 [0%]	6 [0%]	17 [0%]	8 [0%]
rRNA	260 [0.02%]	2,392 [0.23%]	1,990 [0.25%]	1,738 [0.17%]	869 [0.18%]
snRNA	366 [0.03%]	360 [0.03%]	285 [0.04%]	614 [0.06%]	344 [0.07%]
snoRNA	45,052 [4.01%]	22,576 [2.16%]	14,706 [1.81%]	32,513 [3.23%]	15,284 [3.08%]
tRNA	10,031 [0.89%]	13,908 [1.33%]	11,625 [1.43%]	27,266 [2.71%]	13,998 [2.82%]
other	508,035 [45.2%]	237,443 [22.75%]	194,734 [24.01%]	498,318 [49.52%]	248,924 [50.13%]

Overview of sequence data processing by the perl analysis pipeline for the heart tube and embryo samples for the single read (single) and multiplexed (multi) libraries. Total RNA input and smallRNA input samples are indicated with the 'tot' and 's' suffixes, respectively. Indicated from top to bottom are the total number of input sequence reads, sequence reads that were shorter than 15 nt after 3' adapter truncation, sequences accepted for further analysis after 3' adapter truncation, genome alignment classes and the number of sequences annotated to non-coding RNA transcripts. For the genome alignment classes, NM indicates reads that could not be mapped to the genome, R* reads that were mapped to repeat areas and U0-U2, reads that were mapped with either no, one or two mismatches to the genome. Percentages of annotated transcripts are calculated relative to the sum of U0 and U1 reads. The 'other' category indicates reads not annotated to any of the Chicken non-coding RNAs in the Ensembl database.

ISSN: 1471-2164