|
| Status |
Public on Dec 30, 2007 |
| Title |
B. fragilis IB397 5%O2-a2 |
| Sample type |
RNA |
| |
|
| Source name |
IB397 wild type strain stressed with 5% oxygen
|
| Organism |
Bacteroides fragilis |
| Characteristics |
Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397
(wild-type) grown in BHIS complex media and then stressed by shaking in a stoppered
bottle with 5% oxygen atmosphere for 30 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.
|
| Label |
Cy3
|
| Label protocol |
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.
|
| |
|
| Hybridization protocol |
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.
|
| Scan protocol |
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.
|
| Description |
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and
then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were
individually hybridized to the microarray according to the NimbleGen standard operating
procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex
according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm
resolution using an Axon 4000B.
|
| Data processing |
data processed using quantile normalization and RMA algorithm
|
| |
|
| Submission date |
Mar 30, 2006 |
| Last update date |
Sep 27, 2007 |
| Contact name |
Charles Jeffrey Smith |
| E-mail(s) |
smithcha@ecu.edu
|
| Phone |
252-744-2700
|
| Fax |
252-744-3104
|
| Organization name |
East Carolina University
|
| Department |
Microbiology & Immunology
|
| Street address |
600 Moye Blvd.
|
| City |
Greenville |
| State/province |
NC |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL3596 |
| Series (1) |
| GSE4583 |
Bacteroides fragilis oxidative stress |
|
