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Table 2 Transcript coverage

From: Influence of RNA extraction methods and library selection schemes on RNA-seq data

  Categories PolyA Tot RNA Trizol PolyA Tot RNA Qiagen RiboZeroTot RNA Trizol RiboZeroTot RNA Qiagen RiboZero Cytopl. RNA RiboZero Nuclear RNA
Protein coding genes Genes with rpkm ≥ 0.5 12469 12381 12164 12164 12119 12498
Average genes coverage 67% 65% 69% 68% 65% 71%
Genes not covered 2259 2447 2016 2085 2316 1778
Genes ≥50% covered 14345 14144 14540 14540 14038 14978
Genes 100% covered 1677 1468 2287 2072 1370 2892
Genes with only 1 read 263 1468 278 292 287 261
Genes with ≥5 reads 16926 1468 17164 17067 16844 17464
Genes with ≥50 reads 14768 14667 14812 14836 14597 15190
Genes with ≥100 reads 14111 14049 13997 14071 13888 14309
Long non-coding RNAs processed transcript 423 418 452 417 404 532
lincRNA 596 543 625 546 521 927
antisense 914 850 748 748 722 911
sense intronic 97 68 269 269115 87 499
sense overlapping 58 44 57 42 44 87
3 prime overlapping ncrna 20 20 19 19 20 22
non coding 4 3 4 4 4 5
  1. The upper panel lists the number of detected and covered protein coding genes in each category and experimental condition. The panel below lists for each experimental condition the number of detected long non-coding RNA subtypes (rpkm > =0.5).