Sample expression array datasets

Source: Gene Expression Omnibus (GEO)

Transcriptome profiles of a riboflavin-producing B.subtilis RH33 and wild type B.subtilis 168 (PMID: 19446032)

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12873

Overall design:

The transcriptome profiles of a riboflavin-producing recombinant Bacillus subtilis RH33 and wild type Bacillus subtilis 168 were compared using DNA microarrays to identify the target genes for further enhancing riboflavin production.

Samples to compare:

GSM322848 Gene expression of Bacillus subtilis 168 during exponentially growing period_2

GSM322846 Gene expression of Bacillus subtilis 168 during exponentially growing period_1

GSM322847 Gene expression of Bacillus subtilis RH33 during exponentially growing period_1

GSM322849 Gene expression of Bacillus subtilis RH33 during exponentially growing period_2

Gene expression of Pseudomonas aeruginosa during biofilm and planktonic growth (PMID: 19222585)

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE6122

Overall design:

The expression profiles of four planktonically-grown isolates of one Australian clonal strain (AES-1), and four non–clonal CF P. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1.

Samples to compare:

GSM260371 Pseudomonas aeruginosa PAO1 planktonic culture

GSM260372 Pseudomonas aeruginosa PAO1 - biofilm culture

Expression data from P. aeruginosa colonizing the Murine GI Tract (PMID: 21170272)

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE22665

Overall design:

P. aeruginosa was recovered from the drinking water administered to adult C3H/HeN mice and also from cecums of colonized mice, and RNA was extracted and hybridized on Affymetrix microarrays.

Samples to compare:

GSM562112 PAKH2O_1 cells were recovered from the drinking water that was stored in sterile flask for 24h

GSM562113 PAKH2O_2 cells were recovered from the drinking water that was stored in sterile flask for 24h

GSM562114 PAKH2O_3 cells were recovered from the drinking water that was stored in sterile flask for 24h

GSM562109 PAKGIColoniz_1 cells were recovered from murine cecums 7 days after initiating colonization

GSM562110 PAKGIColoniz_2 cells were recovered from murine cecums 7 days after initiating colonization

GSM562111 PAKGIColoniz_3 cells were recovered from murine cecums 7 days after initiating colonization

Adaptation of group A Streptococcus to human amniotic fluid (PMID: 20352104)

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19985

Overall design:

To identify genes that were up or down regulated in response to growth in amniotic fluid (AF), GAS was grown in human AF or standard laboratory media (THY) and samples for expression microarray analysis were collected during mid-logarithmic, late-logarithmic, and stationary growth phases.

Samples to compare:

GSM499302 Group A Streptococcus grown in THY, ML phase replicate 1

GSM499303 Group A Streptococcus grown in THY, ML phase replicate 2

GSM499304 Group A Streptococcus grown in THY, ML phase replicate 3

GSM499361 Group A Streptococcus grown in human amniotic fluid, mid log phase, replicate 1

GSM499362 Group A Streptococcus grown in human amniotic fluid, mid log phase, replicate 2

GSM499363 Group A Streptococcus grown in human amniotic fluid, mid log phase, replicate 3