We deeply appreciate the following studies that have conducted and shared RNA-seq datasets, which have made our work possible.
| Bacteria Species | GSE number | Reference genome | Condition# |
|---|---|---|---|
| Bacillus subtilis | GSE224332, paper | NZ_CP020102.1 | 317 |
| Bacteroides thetaiotaomicron | GSE251676, paper | GCF_000011065.1 | 64 |
| Bordetella hinzii | GSE181542 | CP052845.1 | 228 |
| Caulobacter vibrioides | GSE246782, paper | NC_011916.1 | 34 |
| Cereibacter sphaeroides | GSE186600, paper | GCA_000012905.2 | 17 |
| Chlamydia trachomatis | GSE262652 | GCA_000068585.1 | 30 |
| Clostridioides difficile | GSE249810, paper | GCA_000009205.5 | 24 |
| Clostridium acetobutylicum | GSE107804, paper | GCA_000008765.1 | 48 |
| Clostridium beijerinckii | GSE150480, paper | GCF_000833105.2 | 16 |
| Clostridium butyricum | GSE150480, paper | GCF_001456065.2 | 16 |
| Clostridium tetani | GSE182408, paper | NC_004557.1 | 39 |
| Escherichia coli | GSE152664, paper | NC_010473.1 | 9 |
| Erythrobacter litoralis | GSE126532 | GCA_001719165.1 | 49 |
| Methylotuvimicrobium buryatense | GSE162089, paper | NZ_CP035467.1 | 56 |
| Mycobacterium tuberculosis | GSE110508, paper | GCA_000195955.2 | 87 |
| Mycolicibacterium smegmatis | GSE69983, paper | GCA_000015005.1 | 30 |
| Pseudomonas aeruginosa | GSE251671 | GCA_000014625.1 | 858 |
| Pseudomonas syringae | GSE103441, paper | GCA_000007805.1 | 114 |
| Streptococcus dysgalactiae | GSE272047, paper | GCA_029234115.1 | 114 |
| Streptococcus pyogenes | GSE113055, paper | CP000056.2 | 442 |
| Xanthomonas citri | GSE252662, paper | AE008923.1 | 38 |
| Zymomonas mobilis | GSE139939, paper | CP023715.1 | 19 |
| Archaea Species | GSE number | Reference genome | Condition# |
|---|---|---|---|
| Haloarcula hispanica | GSE227031 | GCF_000223905.1 | 32 |
| Halobacterium salinarum | GSE182493, paper | GCF_000006805.1 | 24 |
| Haloferax volcanii | GSE248564, paper | GCF_000025685.1 | 39 |
| Methanocaldococcus jannaschii | GSE112986, paper | GCF_000091665.1 | 13 |
| Methanococcus maripaludis | GSE261517, paper | GCF_000011585.1 | 12 |
| Methanosarcina barkeri | GSE168895, paper | GCF_000970025.1 | 12 |
| Nitrosopumilus maritimus | GSE103699 | GCA_000018465.1 | 7 |
| Sulfolobus islandicus | GSE220819, paper | GCF_000189555.1 | 18 |
| Thermococcus kodakarensis | GSE186817 | NC_006624.1 | 4 |
| Thermococcus paralvinellae | GSE101078, paper | GCF_000517445.1 | 15 |
| Species | Reference | Reference genome | Condition# |
|---|---|---|---|
| Acinetobacter baumannii | Menon, et al., paper | CP008706.1 | 139 |
| Bacillus subtilis | Sastry, et al. | NC_000964.3 | 265 |
| Escherichia coli | Lamoureux, et al., paper | U00096.3 | 1035 |
| Limosilactobacillus reuteri | Josephs-Spaulding, et al., paper | GCA_020785475.1 | 117 |
| Mycobacterium tuberculosis | Yoo, et al., paper | AL123456.3 | 647 |
| Pseudomonas aeruginosa | Rajput, et al., paper | NC_002516.2 | 411 |
| Pseudomonas putida | Lim, et al., paper | AE015451.2 | 321 |
| Pseudomonas syringae | Bajpe, et al., paper | AE016853.1 | 202 |
| Staphylococcus aureus | Poudel, et al., paper | NC_010079.1 | 385 |
| Synechococcus elongatus | Yuan, et al., paper | NC_007604.1 | 300 |
| Salmonella enterica | Yuan, et al., paper | AE006468.2 | 533 |
| Streptococcus pyogenes | Hirose, et al., paper | CP008776.1 | 116 |
| Vibrio natriegens | Shin, et al., paper | GCA_001456255.1 | 148 |