|
| Status |
Public on Feb 09, 2010 |
| Title |
WGA, NCFM, 10 ml (C), 1 ml (T) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
NCFM_log phase_10 ml
|
| Organism |
Lactobacillus acidophilus |
| Characteristics |
Non-concentrated, incubated (1h 37°C) log-phase cultures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Azcarate-Peril et al., 2005
|
| Label |
Cy3
|
| Label protocol |
see TIGR Microarray Protocols and Standard Operating Procedures website
|
| |
|
| Channel 2 |
| Source name |
NCFM_log phase_1 ml
|
| Organism |
Lactobacillus acidophilus |
| Characteristics |
10-fold concentrated, incubated (1h 37°C) log-phase cultures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Azcarate-Peril et al., 2005
|
| Label |
Cy5
|
| Label protocol |
see TIGR Microarray Protocols and Standard Operating Procedures website
|
| |
|
| |
| Hybridization protocol |
see TIGR Microarray Protocols and Standard Operating Procedures website
|
| Scan protocol |
Fluorescence intensities were acquired using a General Scanning ScanArray 4000 Microarray Scanner (Packard Biochip BioScience, Biochip Technologies LLC, Mas.) and processed as TIFF images.
|
| Description |
The ratio between the average absolute pixel values for the replicated spots of each gene with and without treatment represented the fold change in gene expression. Confidence intervals and P values on the fold change were also calculated with the use of a two-sample t test. P values of 0.05 or less were considered significant
|
| Data processing |
Signal intensities were quantified using the QuantArray 3.0 software package (Packard BioScience). The local background was subsequently subtracted from the recorded spot intensities. Data was median normalized.
|
| |
|
| Submission date |
Aug 30, 2006 |
| Last update date |
Feb 09, 2009 |
| Contact name |
Todd Robert Klaenhammer |
| E-mail(s) |
trk@ncsu.edu, yjgoh@ncsu.edu, sjoflahe@ncsu.edu
|
| Phone |
919-515-2972
|
| Fax |
919 513 0014
|
| Organization name |
North Carolina State University
|
| Department |
Department of Food, Bioprocessing, and Nutrition Sciences
|
| Street address |
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL1401 |
| Series (1) |
| GSE5674 |
Influence of environmental conditions and AI2 on the adhesion adaptive response of Lactobacillus acidophilus NCFM |
|
| Data table header descriptions |
| ID_REF |
|
| RATIO |
(Cy5 Normalized - Background) / (Cy3 Normalized -Background) |
| VALUE |
log ratio (log2 of RATIO) |
| CH1_RAW |
raw signal output for channel 1 |
| CH1_BKD |
background signal output for channel 1 |
| CH1_SD |
standard deviation calculated for the mean signal for channel 1 |
| CH1_BKD_SD |
standard deviation for the mean background signal for channel 1 |
| CH2_RAW |
raw signal output for channel 2 |
| CH2_BKD |
background signal output for channel 2 |
| CH2_SD |
standard deviation calculated for the mean signal for channel 2 |
| CH2_BKD_SD |
standard deviation for the mean background signal for channel 2 |
