|
Status |
Public on Dec 30, 2007 |
Title |
B. fragilis IB397 H2O2-c1 |
Sample type |
RNA |
|
|
Source name |
IB397 wild type strain stressed with H2O2
|
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 stressed with 50 micromolar H2O2 two times for 15 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 |
Feb 26, 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 |
|