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Table 2 List of the number of raw reads of 8 replicates from (A) CLC, (B) DNAstar-E, (C) DNAstar-D after cutoff < 30 reads from E. coli . M1-4 = 4 reps from Minus radiation treatment, K1-4 = 4 reps from the KCl-amended treatment. (Note that since we only used the Partek trial version, we had no opportunity to change cutoff values.)

From: A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

(A)
Name Fold change total gene reads_M1 total gene reads_M2 total gene reads_M3 total gene reads_M4 total gene reads_K1 total gene reads_K2 total gene reads_K3 total gene reads_K4
gadA -26 350 174 147 82 20385 2386 617 534
gadB -22 265 84 68 36 9767 1439 508 333
asr -17 5819 4929 909 150 2E+05 30951 11582 14226
adiA -16 866 256 242 124 24125 3282 682 780
hdeB -10 1223 351 568 112 16335 6740 2361 2789
adiC -10 1022 241 229 68 13876 2768 888 705
(B)
Name Fold change total gene reads_M1 total gene reads_M2 total gene reads_M3 total gene reads_M4 total gene reads_K1 total gene reads_K2 total gene reads_K3 total gene reads_K4
gadA -26 669 323 270 144 38573 4581 1227 999
gadB -23 561 201 161 94 21956 3104 1024 742
asr -17 11721 9846 1774 295 356439 60822 22952 28811
adiA -17 1724 496 479 246 48188 6568 1368 1569
hdeB -11 2154 620 1020 186 28362 11768 4096 4844
adiC -10 2044 465 452 135 27841 5547 1760 1392
(C)
Name Fold change total gene reads_M1 total gene reads_M2 total gene reads_M3 total gene reads_M4 total gene reads_K1 total gene reads_K2 total gene reads_K3 total gene reads_K4
gadA -1 669 323 270 144 38573 4581 1227 999
gadB -2 561 201 161 94 21956 3104 1024 742
asr -1 11721 9846 1774 295 356439 60822 22952 28811
adiA -1 1724 496 479 246 48188 6568 1368 1569
hdeB -2 2154 620 1020 186 28362 11768 4096 4844
adiC NS 2044 465 452 135 27841 5547 1760 1392