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 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
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 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
No. of read pairs (2 x 100Â 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 | - |