|
| Status |
Public on Dec 10, 2013 |
| Title |
at 40 mins during the HLOT condition |
| Sample type |
RNA |
| |
|
| Source name |
at 40 mins during the HLOT condition
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
time: 40 mins
treatment: the oxygen-availability transition from oxygen replete (high oxygen tension, 100%) to oxygen deplete condition (low oxygen tension, 0.5%).
|
| Treatment protocol |
In order to stabilize RNA immediately, the samples from chemostat culture of PA were directly flushed into pre-cooled RNAprotect Bacteria Reagent (Qiagen) and treated instantly as suggested by the supplier before stored at -80°C for later RNA isolation.
|
| Growth protocol |
Pseudomonas aeruginosa PAO1 (PA) was grown in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted by using the RNeasy mini kit including an on-column DNase treatment according to the manufacturer’s instructions (Qiagen). The RNA concentration and purity were determined using the 2100 Bioanalyser (Agilent). A total of 10 μg of each experimental RNA sample was used for cDNA synthesis with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). DNaseI (Pierce) and 10-fold One-Phor-All Buffer (GE healthcare) were used for cDNA fragmentation.
|
| Label |
biotin
|
| Label protocol |
The Enzo BioArray terminal labeling kit (Affymetrix) was used for labeling the fragmented cDNA with a size range from 50-200 bp. The fragmentation and labeling effect were checked by gel electrophoresis.
|
| |
|
| Hybridization protocol |
The cDNA was loaded onto Affymetrix PA GeneChip. Target hybridization was performed at 37 °C for 16 hours by using a GeneChip Hybridization Oven 640. Chip washing and staining were performed with an Affymetrix GeneChip Fluidics Station 400
|
| Scan protocol |
The chips were scanned with Agilent Genearray Scanner. The scanned images were analyzed using the Affymetrix GCOS program 1.2.
|
| Description |
HLOT40
time-series gene expression data from Pseudomonas aeruginosa PAO1
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 150.
MAS5.0 signal intensity, detection call (ABS_CALL), and detection P-value by MAS5.0 method (default setting) are reported.
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| |
|
| Submission date |
Nov 18, 2013 |
| Last update date |
Dec 11, 2013 |
| Contact name |
Feng Q. Hefeng |
| E-mail(s) |
[email protected]
|
| Organization name |
Luxembourg Institute of Health
|
| Department |
Department of Infection and Immunity
|
| Street address |
29, rue Henri Koch
|
| City |
Esch-sur-Alzette |
| ZIP/Postal code |
4354 |
| Country |
Luxembourg |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE52445 |
High-time-resolution time-series transcriptome data of Pseudomonas aeruginosa PAO1 under two inverted oxygen-availability transitions |
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