|
| Status |
Public on Oct 05, 2012 |
| Title |
MC58 wild type compared to mc58 zur knock out mutant 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from strain MC58 grown in RPMI
|
| Organism |
Neisseria meningitidis |
| Characteristics |
genotype: wild type
treatment: none
sample type: RNA isolated from the RPMI grown strain using RNeasy kit from Qiagen
strain: MC58
|
| Growth protocol |
The strains were grown in RPMI 1640 medium to a mid log phase with and without Zinc supplementation and 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 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 |
RNA from strain MC58 zur knock out grown in RPMI
|
| Organism |
Neisseria meningitidis |
| Characteristics |
genotype: zur KO
treatment: none
sample type: RNA isolated from the adherent strain using RNeasy kit from Qiagen
strain: MC58
|
| Growth protocol |
The strains were grown in RPMI 1640 medium to a mid log phase with and without Zinc supplementation and 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 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 |
MC58 zur knock out versus MC58 wild type_Replicate_2_dye swap
|
| 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 17, 2012 |
| Last update date |
Oct 05, 2012 |
| 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) |
| GSE38033 |
Zur regulon of Neisseria meningitidis |
|
