|
| Status |
Public on Aug 25, 2009 |
| Title |
2221sRNA3 |
| Sample type |
RNA |
| |
|
| Source name |
MGAS2221 culture 3 grown to an O.D.600 of 0.5
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
strain: MGAS2221
serotype: M1 GAS
growth phase: exponential phase
|
| Treatment protocol |
Two volumes of RNAprotect was added to each culture, incubated at RT for 5 mins, centrifuged, a bacterial cell pellet quick frozen in liquid nitrogen.
|
| Growth protocol |
MGAS2221 cultures were grown in THY broth to O.D. 600 of 0.5 (exponential phase).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted via mechanical disruption and purified using the Qiagen Rneasy kit.
|
| Label |
biotin
|
| Label protocol |
RNA was converted to cDNA, the cDNA was fragmented, and the cDNA labeled with biotin.
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized to a custom array for 16h at 40 degrees C. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using a GeneArray Scanner G2500A.
|
| Description |
MGAS2221 chip 3
|
| Data processing |
Data was quantile normalized and analyzed with Tiling Analysis Software (TAS). Data from the three arrays were combined to generate signal intensities. Signal and p-values are reported in BAR files, which are linked to the Series GSE17789 record as supplementary files.
The BAR files are generated by TAS software using PM/MM signal intensities. Signal intensity data is reported in a linear scale while the p-value is reported in -10log10 scale. Probe analysis used a bandwidth of 40. Interval analysis used a threshold of 0, a maximum gap of 20, and a minimum run of 60.
|
| |
|
| Submission date |
Aug 24, 2009 |
| Last update date |
Aug 24, 2009 |
| Contact name |
Paul Sumby |
| Organization name |
University of Nevada
|
| Department |
Microbiology & Immunology
|
| Street address |
1554 N. Virginia St.
|
| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL6186 |
| Series (2) |
| GSE17789 |
Tiling microarray-based identification of small regulatory RNAs in the group A Streptococcus (GAS) |
| GSE17790 |
A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus |
|
