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Status |
Public on Aug 06, 2011 |
Title |
CF333-1997 isolate, biological rep2 |
Sample type |
RNA |
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|
Source name |
CF333 patient 1997 isolate
|
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).
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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.
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Description |
CF333-1997b
|
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.
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|
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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 |
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