|
| Status |
Public on Aug 06, 2011 |
| Title |
B12-4 isolate, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
B12 patient isolate at month 4
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: Gram-negative
|
| Treatment protocol |
Harvested cells were mixed immediately with RNAprotect Bacteria Reagent (Qiagen) and stored at −80 °C.
|
| Growth protocol |
P. aeruginosa strains were grown aerobically at 37 °C in LB medium starting from OD600 = 0.01 and harvested at OD600 = 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with an RNeasy Mini Kit (Qiagen) and transcribed to cDNA using a SuperScript III Reverse Transcriptase (Invitrogen).
|
| Label |
biotin-ddUTP
|
| Label protocol |
The cDNA was synthezed from RNA, purified with a Qiagen PCR Purification Kit (Qiagen) and fragmented using DNase I (Promega). Fragmented cDNA was then labeled with biotinylated nucleotides at the 3' termini using labeling reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega).
|
| |
|
| Hybridization protocol |
The labeled cDNA was hybridized on an Affymetrix P. aeruginosa PAO1 gene chip and stained on a GeneChip Fluidics Station 450.
|
| Scan protocol |
The probe arrays were finally scanned with a GeneChip Scanner 3000.
|
| Description |
B12-4_2
|
| Data processing |
The raw data (.cel files) were obtained using the Affymetrix GeneChip Operating System 1.4. The raw data files are preprocessed by Bioconductor using the RMA method.
|
| |
|
| Submission date |
Aug 05, 2011 |
| Last update date |
Aug 06, 2011 |
| Contact name |
Liang Yang |
| E-mail(s) |
ly@bio.dtu.dk
|
| Organization name |
Technical University of Denmark
|
| Street address |
Building 301, Room 150
|
| City |
Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE31227 |
Expression data of Pseudomonas aeruginosa isolates from Cystic Fibrosis patients in Denmark |
|
