|
| Status |
Public on May 04, 2015 |
| Title |
The nox Complemented Strain Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from the nox complemented strain at exponential growth phase
|
| Organism |
Streptococcus sanguinis |
| Characteristics |
strain: nox complemented strain
|
| Treatment protocol |
The cultures at exponential phase were haversted and used for RNA isolation.
|
| Growth protocol |
The nox mutant was grown in BM medium at 37 °C ovenight under anaerobic conditions. The overnight cultures were diluted 1:100 in BM medium and incubated under the same conditions as above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Aminoallyl-labeled cDNA was labeled by Cy5 for test or Cy3 for reference as described in the manual for microbial RNA aminoallyl labeling for microarrays at The J. Craig Venter Institute.
|
| |
|
| Channel 2 |
| Source name |
Total RNA from the wild-type strain SK36 at exponential growth phase
|
| Organism |
Streptococcus sanguinis |
| Characteristics |
strain: SK36
|
| Treatment protocol |
The cultures at exponential phase were haversted and used for RNA isolation.
|
| Growth protocol |
The nox mutant was grown in BM medium at 37 °C ovenight under anaerobic conditions. The overnight cultures were diluted 1:100 in BM medium and incubated under the same conditions as above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Aminoallyl-labeled cDNA was labeled by Cy5 for test or Cy3 for reference as described in the manual for microbial RNA aminoallyl labeling for microarrays at The J. Craig Venter Institute.
|
| |
|
| |
| Hybridization protocol |
After prehybridization, spotted microarray was hybridized with Cy3- and Cy5-labeled cDNA for 16 h at 42 °C according to the protocol for hybridization of labeled DNA and cDNA probes at The J. Craig Venter Institute
|
| Scan protocol |
Hybridized microarray was scanned using GenePix 4200A Scanner (Axon Instruments).
|
| Description |
Biological replicate 1 of 3.
nox-compl-1
|
| Data processing |
Images were quantified using TIGR Spotfinder Software (version 3.2.1). Data were filtered and LOWESS normalized by TIGR Midas Software (version 2.22).
|
| |
|
| Submission date |
May 04, 2015 |
| Last update date |
May 04, 2015 |
| Contact name |
Xiuchun Ge |
| Organization name |
Virginia Commonwealth University
|
| Street address |
521 North 11th Street
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL14967 |
| Series (1) |
| GSE68492 |
Differential expression of genes in Streptococcus sanguinis nox mutant and its complemented strain |
|
