Bacillus anthracis Ames (1 series, 12 samples)
GSE22559
Transcriptome comparison of B. anthracis Ames and isogenic sinR-null mutant,
UTA21
Bacillus subtilis str. 168 (3 series, 27 samples)
GSE11810
Base and acid resistance of B. subtilis associated with transcriptomic
responses
GSE12263
Benzoate induced transcriptomic response in Bacillus subtilis
GSE12873
Transcriptome profiles of a riboflavin-producing B.subtilis RH33 and wild type
B.subtilis 168
Bacteroides thetaiotaomicron VPI-5482 (3 series, 41 samples)
GSE11962
Growth of B. thetaiotaomicron on purified host mucosal glycans and glycan
fragments
GSE14709
Transcriptional profile of B. theta and E. rectale growing in the cecum of mice
fed different diets
GSE14737
Characterizing a model human gut microbiota composed of members of its two
dominant bacterial phyla
Bradyrhizobium japonicum (10 Series, 195 Samples)
GSE8478
Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in
soybean root nodules (removed 3 soybean controls)
GSE8570
Comparison of B. japonicum mutant strain Δ901 induced versus wild type
uninduced
GSE8571
Comparison of B. japonicum 110spc4 (wild type) induced versus uninduced
GSE9026
New target genes controlled by the Bradyrhizobium japonicum two-component
regulatory system RegSR
GSE8572
Comparison of B. japonicum mutant strain 613 induced versus wild type uninduced
GSE11187
Global consequences of phosphatidylcholine reduction in Bradyrhizobium
japonicum
GSE12491
Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1
cascade in Bradyrhizobium japonicum
GSE15910
The PhyR-sigmaEcfG signaling cascade is involved in stress response and
symbiotic efficiency in Bradyrhizobium japonicum
GSE18884
Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis
GSE21400
Autoregulation of fixK2 gene expression in Bradyrhizobium japonicum
E. coli K12 (907 Samples downloaded
from M3D)
Project information page at M3D is here .
Unfortunately there doesn’t appear to be any easy way to determine which
samples go with which project. It may be necessary to look up the
references for each project and see if they state the names of the samples
associated with the project. For samples with names that start with GSM,
it is also possible to search GEO
for that GSM identifier.
Eubacterium rectale (2 series, 27 samples)
GSE14709
Transcriptional profile of B. theta and E. rectale growing in the cecum of mice
fed different diets
GSE14737
Characterizing a model human gut microbiota composed of members of its two
dominant bacterial phyla
Helicobacter pylori HPAG1 (2 series, 56 samples)
GSE10261
Expression data from Helicobacter pylori isolates infecting a gastric
epithelial progenitor cell line
GSE16439
Response of gastric epithelial progenitors to H. pylori isolates from Swedish
patients with chronic atrophic gastritis 2 (removed controls with no H. pylori)
Mycoplasma pneumoniae M129 (2 series, 43 samples)
GSE14014
Mycoplasma pneumoniae transcriptome analysis
GSE14019
Transcriptome/Expression analysis in Mycoplasma pneumoniae
Neisseria gonorrhoeae (1 series, 24 samples)
GSE16352
Transcriptional analysis of the Neisseria gonorrhoeae Fur regulon
Pasteurella multocida subsp. multocida str. Pm70 (1 series,
72 samples)
GSE10051
A compendium of antibiotic-induced transcription profiles reveals broad
regulation of P. multocida virulence genes
Pseudomonas aeruginosa PA01 (multiple series, 176 samples)
Series descriptions are available here
in GEO by clicking on “More” under the
“Series (57)” label. We only used series that involve the PA01 strain.
Rhodobacter sphaeroides (12 series, 119 samples)
Series descriptions are available here
in GEO by clicking on “More” under the
“Series (15)” label. We used the following series:
GSE139,
GSE532,
GSE1480,
GSE1515,
GSE2145,
GSE2146,
GSE2219,
GSE9534,
GSE8082,
GSE20337,
GSE22063,
GSE12269
Rickettsia rickettsii (1 series, 100 samples)
GSE14965
Limited transcriptional responses of Rickettsia rickettsii exposed to
environmental stimuli
Rhodopseudomonas palustris CGA009 (3 series, 24 samples)
Series descriptions are available here
in GEO by clicking on “More” under the
“Series (3)” label.
Shewanella oneidensis MR-1 (245 CELs from M3D database)
Project information page at M3D is here .
Unfortunately there doesn’t appear to be any easy way to determine which
samples go with which project. It may be necessary to look up the
references for each project and see if they state the names of the samples
associated with the project. For samples with names that start with GSM,
it is also possible to search GEO
for that GSM identifier.
Staphylococcus aureus (852 samples from Paul Dunman)
No descriptions available. For samples with names that
start with GSM, it is also possible to search GEO
for that GSM identifier.
Streptococcus agalactiae (5 series, 78 samples)
Series descriptions are available here
in GEO by clicking on “More” under the
“Series (5)” label.
Streptococcus pyogenes (6 series, 89 samples)
GSE17767
Transcriptome comparison of Streptococcus pyogenes strain MGAS2221 with that of
an isogenic PEL mutant
GSE17789
Tiling microarray-based identification of small regulatory RNAs in the group A
Streptococcus (GAS)
GSE9793
Expression comparison between MGAS2221 and isogenic spyCEP mutant
GSE10156
Analysis of the group A Streptococcus CcpA Transcriptome
GSE20212
Comparison of the CcpA and CovR Transcriptomes in Group A Streptococcus
GSE19985
Adaptation of group A Streptococcus to human amniotic fluid
Streptomyces coelicolor (1 series, 55 samples)
GSE18489
Metabolic switching in Streptomyces coelicolor Timeseries 1
Synechococcus elongatus (1 series, 104 samples)
GSE14225
Circadian and diurnal expression data of Synechococcus
Thermus thermophilus (44 series, 407 samples)
Series descriptions are available here
in GEO by clicking on “More” under the
“Series (44)” label.
Vibrio fischeri (2 series, 20 samples)
GSE7485
A transcriptome analysis of the Vibrio fischeri LuxR-LuxI regulon
GSE15522
Expression data of Vibrio fischeri in response to nitric oxide (NO)
Vibrio parahaemolyticus RIMD 2210633 (2 series, 42
samples)
GSE18763 Surface sensing in
Vibrio parahaemolyticus triggers a programme of gene expression that promotes
colonization and virulence
GSE22190
Calcium is a global regulator in Vibrio parahaemolyticus