|
| Status |
Public on Mar 06, 2006 |
| Title |
Time course analysis of genes regulated by E. coli sigma 32 (rpoH) after overexpression |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by array
|
| Summary |
DNA microarray analysis of genes regulated by the alternative sigma factor, sigma 32 (rpoH). Sigma 32-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma 32, with a strain over-expressing sigma 32 (following induction of rpoH from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses. Because sigma 32 is negatively regulated, its activity decreases 10 min after overexpression. Consequently, to identify genes regulated by sigma 32 we analyzed the expression data for 10 min after overexpression using SAM (Statistical Analysis of Microarrays). We identified 105 genes organized in 66 separate transcription units. This study is detailed in Nonaka et al 2006 (submitted).
Keywords: time course
|
| |
|
| Overall design |
This series consists of 4 replicated time courses from separate biological samples. Each time course consists of a comparison between wild type E.coli MG1655 that has a low level of sigma 32, and an over-expressing sigma 32 strain following induction of rpoH from an inducible promoter by IPTG. Both strains were grown to mid log and then induced with IPTG and incubation resumed. Samples were removed for comparative microarray analysis immediately prior to induction, and at 2.5, 5, 10, and 20 min after induction. To correct for changes in growth state, control and over-expressed samples were always compared from the same time point. Note time course 4 only contains the 10 min samples.
|
| |
|
| Contributor(s) |
Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA |
| Citation(s) |
16818608 |
| |
| Submission date |
Mar 01, 2006 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Virgil Arthur Rhodius |
| E-mail(s) |
[email protected]
|
| Phone |
1 415 476 1493
|
| URL |
http://www.ucsf.edu/gross
|
| Organization name |
UCSF
|
| Department |
Microbiology and Immunology
|
| Lab |
Gross
|
| Street address |
Genentech Hall, 600 16th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158-2517 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (16)
|
| GSM98717 |
EC18n177 RpoH 0 min Time course 1 |
| GSM98718 |
EC18n178 RpoH 2.5 min Time course 1 |
| GSM98719 |
EC18n179 RpoH 5 min Time course 1 |
| GSM98720 |
EC18n180 RpoH 10 min Time course 1 |
| GSM98721 |
EC18n181 RpoH 20 min Time course 1 |
| GSM98722 |
EC18n167 RpoH 0 min Time course 2 |
| GSM98723 |
EC18n168 RpoH 2.5 min Time course 2 |
| GSM98724 |
EC18n169 RpoH 5 min Time course 2 |
| GSM98725 |
EC18n170 RpoH 10 min Time course 2 |
| GSM98726 |
EC18n171 RpoH 20 min Time course 2 |
| GSM98727 |
EC18n182 RpoH 0 min Time course 3 |
| GSM98728 |
EC18n183 RpoH 2.5 min Time course 3 |
| GSM98729 |
EC18n184 RpoH 5 min Time course 3 |
| GSM98730 |
EC18n185 RpoH 10 min Time course 3 |
| GSM98731 |
EC18n186 RpoH 20 min Time course 3 |
| GSM98732 |
EC18n122 RpoH 10 min Time course 4 |
|
| Relations |
| BioProject |
PRJNA94741 |
Less...
More...