|
| Status |
Public on Feb 09, 2017 |
| Title |
phoP-stationary phase-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
phoP-stationary phase-rep2
|
| Organism |
Yersinia pestis |
| Characteristics |
genotype: phoP mutant
strain: KIM6
treatment: stationary phase
|
| Treatment protocol |
no treatments, just strain differences
|
| Growth protocol |
The bacterial100 strains used in this study were Y. pestis KIM6+, which lacks the 70-kb virulence plasmid that is not required for flea infection or blockage, and an isogenic mutant deleted of functional phoP. For in vitro planktonic samples, bacteria were grown from frozen stocks in Brain Heart Infusion (BHI) broth at 28°C, followed by two successive transfers in Luria Bertani broth supplemented with 100 mM MOPS, pH 7.4 (LB/MOPS) at 21°C. An inoculum of 104 cells/ml was added to 50 ml of LB/MOPS and incubated at 21°C with shaking at 250 rpm until exponential (OD600 = 2.5) or stationary phase (OD600 = 4.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from five independent samples from in vitro and flow cell cultures and from pooled fleas two weeks post-infection, using the RNeasy Mini Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Total RNA (100 ng) was amplified and labeled with biotin-16-UTP (Roche Molecular Biochemicals, Pleasanton, CA) by using the Message-Amp II-Bacteria amplified antisense RNA (aRNA) kit (Ambion; Austin, TX). Amplified RNA was then fragmented using Ambion’s Fragmentation reagent (Applied Biosystems)
|
| |
|
| Hybridization protocol |
All cRNAs were hybridized to a custom Affymetrix GeneChip
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.
|
| Description |
Gene expression data from phoP-stationary phase-rep2
|
| Data processing |
The data were analyzed with Expression Console
MAS5.0 signal intensity
|
| |
|
| Submission date |
Sep 18, 2014 |
| Last update date |
Feb 09, 2017 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL2129 |
| Series (1) |
| GSE61558 |
Role of the PhoP-PhoQ Gene Regulatory System in Adaptation of Yersinia pestis to Environmental Stress in the Flea Digestive Tract |
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