Table 1

Overview over smRNA and mRNA sequencing and assembly statistics
Library name 4°C 16°C 34°C 36°C 20 g 60 g DC DS Noon
Experimental treatment [4°C 4hs] [16°C 4hs] [34°C 12hs] [36°C 4hs] [20 g/L NaCl 4hs] [60 g/L NaCl 4hs] [midnight] [24hs dark] [reference]
smRNA
Total base pairs 476,999,446 327,143,288 185,735,770 254,824,059 427,785,834 220,539,256 258,016,695 133,416,325 361,512,933
No. of reads (after trimming) 17,193,220 12,593,192 8,433,048 10,658,877 15,378,342 8,725,667 10,662,995 6,131,326 13,591,577
Mean read length 28 26 22 24 28 25 24 22 27
No. of reads (after smRNA filtering) 16,404,546 12,102,929 8,234,625 10,180,915 14,747,100 8,399,643 10,259,502 6,025,546 13,017,083
No. of unique reads 2,288,514 2,198,132 1,633,046 2,338,445 2,352,632 1,705,659 1,964,913 1,405,173 1,881,585
No. of miRNAs (miRDeep2) 118 96 131 114 136 104 129 115 138
Mean readcount of miRNAs 149 418 300 199 257 170 253 171 446
No. of miRNAs w/ miRNA* (miRDeep2) 55 83 84 66 61 70 77 75 81
No. of miRNAs (after manual inspection) 21 21 21 21 21 21 21 21 21
mRNA
No. of read pairs (2 x 100 bp) 26,119,370 34,506,164 41,918,850 30,712,175 39,211,121 34,918,126 28,787,997 36,782,164 29,985,278
No. read pairs mapped 16,777,195 23,084,001 27,761,160 19,905,837 24,920,330 23,277,719 19,357,409 24,141,222 20,023,519
No. of 58,649 genes expressed (FPKM > 0) 55,881 56,353 57,389 55,518 55,287 56,526 56,292 56,041 56,778
No. of 58,649 genes expressed (FPKM > 5) 40,078 39,125 39,246 37,256 37,435 39,198 38,041 38,422 40,206
Median FPKM 12.58 12.29 11.87 11.42 11.13 12.38 11.41 11.66 12.49
BLASTX annotation [%] 44.81 44.51 43.80 45.10 45.39 44.44 44.59 44.81 44.18
Pfam [%] 34.50 34.23 33.63 34.71 34.87 34.13 34.27 34.43 33.98
GO annotation [%] 34.90 34.67 34.08 35.14 35.32 34.59 34.71 34.89 34.39
DEGs all (vs. noon) 119 37 351 2,465 138 48 67 60 -
DEGs up (vs. noon) 47 12 105 293 21 14 22 28 -
DEGs down (vs. noon) 72 25 246 2,172 117 34 45 32 -
log2 difference (minimum/maximum) −8.30/+6.61 −7.27/+5.27 −6.84/+7.34 −8.43/+8.17 −10.43/+5.46 −7.02/+6.24 −7.32/+5.19 −7.06/+7.64 -
log2 difference (mean) 2.93 3.15 2.29 2.79 2.73 3.27 2.99 3.01 -

DEG = Differentially Expressed Gene.

Baumgarten et al.

Baumgarten et al. BMC Genomics 2013 14:704   doi:10.1186/1471-2164-14-704

Open Data