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.

Buermans et al. BMC Genomics 2010 11:716   doi:10.1186/1471-2164-11-716

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