BMC Genomics

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

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ISSN: 1471-2164

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