|
| Status |
Public on Dec 31, 2016 |
| Title |
Strain_α522_Saliva replicate3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from strain α522 grown in PPM+ and exposed to human saliva
|
| Organism |
Neisseria meningitidis |
| Characteristics |
strain: α522
exposure: PPM+ grown and exposed to human saliva strain using Trizol
|
| Growth protocol |
The strains were grown in PPM+ medium to a mid log phase and harvested for RNA isolation. For isolation of RNA from the strains on exposure to human material, the cells were harvested and exposed to human saliva, blood or csf for 30 minutes and cells were harvested for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNeasy kit from Qiagen following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
10 µg of test RNA and 10 µg of common reference RNA were labelled with Cy3 dCTP and Cy5 dCTP using reverse transcriptase (Invitrogen)and random nonamers and the labelled DNA was precipitated and purified.
|
| |
|
| Channel 2 |
| Source name |
Common Reference
|
| Organism |
Neisseria meningitidis |
| Characteristics |
reference: Pool of all individual RNA´s
|
| Growth protocol |
The strains were grown in PPM+ medium to a mid log phase and harvested for RNA isolation. For isolation of RNA from the strains on exposure to human material, the cells were harvested and exposed to human saliva, blood or csf for 30 minutes and cells were harvested for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNeasy kit from Qiagen following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
10 µg of test RNA and 10 µg of common reference RNA were labelled with Cy3 dCTP and Cy5 dCTP using reverse transcriptase (Invitrogen)and random nonamers and the labelled DNA was precipitated and purified.
|
| |
|
| |
| Hybridization protocol |
The labelled DNA were mixed together in hybridization buffer (3 x SSC and 0.1% SDS) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.
|
| Scan protocol |
The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.
|
| Description |
replicate 3 of 3
|
| Data processing |
Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma. Loess normalization was used for within slide and Rquantile normalization was used for between slide normalization.
|
| |
|
| Submission date |
May 18, 2012 |
| Last update date |
Dec 31, 2016 |
| Contact name |
Biju Joseph Ampattu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Wuerzburg
|
| Department |
Department of Microbiology
|
| Street address |
Josef-Schneider Str 2
|
| City |
Wuerzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8787 |
| Series (1) |
| GSE38051 |
Neisseria meningitidis strain MC58 and α522 grown in PPM+ and exposed to human saliva, human whole blood and human cerebrospinal fluid |
|
